RCSB PDB Data Deposition Tools at a glance:

SF-Tool Check coordinates against structure factor data and convert various structure factor file formats (formerly Crystallographic Data Validation)
pdb_extract annotation tool Prepare coordinate and structure factor files for deposition
Validation server
Validate your structure at any time
ADIT server
ADIT-NMR server
or try ADITBeta!
Assemble, validate and deposit coordinate and experimental data
Ligand Expo
Search for ligands present in the chemical component dictionary (formerly Ligand Depot)
Standalone pdb_extract Prepare coordinate and structure factor files on your desktop
Standalone Validation Validate a coordinate file at any stage of structure determination on your desktop
Standalone ADIT Assemble, validate and generate mmCIF files on your desktop ready for deposition