1XJQ

ADP Complex OF HUMAN PAPS SYNTHETASE 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X6VPDB ENTRY 1X6V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62901 mM ADP was soaked into native crystals (PDB ENTRY 1X6V) for one hour, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.5α = 90
b = 82.5β = 105
c = 133γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.052097.50.1040.08313.67.4100470
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.189.50.6090.7412.485.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT WITH INITIAL MERCURY PHASESTHROUGHOUTPDB ENTRY 1X6V2.06129.110047092501486996.560.173830.171350.22147RANDOM37.726
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.61.220.77-1.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.54
r_scangle_it3.694
r_mcangle_it3.549
r_angle_refined_deg2.474
r_scbond_it2.411
r_mcbond_it2.303
r_angle_other_deg1.319
r_symmetry_hbond_refined0.287
r_nbd_other0.283
r_symmetry_vdw_other0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.54
r_scangle_it3.694
r_mcangle_it3.549
r_angle_refined_deg2.474
r_scbond_it2.411
r_mcbond_it2.303
r_angle_other_deg1.319
r_symmetry_hbond_refined0.287
r_nbd_other0.283
r_symmetry_vdw_other0.249
r_nbd_refined0.247
r_xyhbond_nbd_refined0.235
r_symmetry_vdw_refined0.2
r_chiral_restr0.162
r_nbtor_other0.107
r_bond_refined_d0.034
r_bond_other_d0.029
r_gen_planes_other0.018
r_gen_planes_refined0.016
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9206
Nucleic Acid Atoms
Solvent Atoms684
Heterogen Atoms81

Software

Software
Software NamePurpose
X-GENdata scaling
XDSdata reduction
XFITdata reduction
REFMACrefinement
X-GENdata reduction
XDSdata scaling