X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NPC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M Na/K PO4, 20% PEG3,350
Crystal Properties
Matthews coefficientSolvent content
2.1843.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.004α = 90
b = 102.004β = 90
c = 70.088γ = 90
Symmetry
Space GroupP 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97915SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.1519.61699.80.14110.89.139267
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.221.269

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3npc2.1519.61639264192999.7940.2860.28420.327436.292
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]
0.7030.703-1.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.273
r_dihedral_angle_4_deg17.112
r_dihedral_angle_3_deg16.065
r_dihedral_angle_1_deg6.748
r_lrange_it5.027
r_lrange_other5.024
r_mcangle_it2.982
r_mcangle_other2.981
r_scangle_it2.928
r_scangle_other2.927
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.273
r_dihedral_angle_4_deg17.112
r_dihedral_angle_3_deg16.065
r_dihedral_angle_1_deg6.748
r_lrange_it5.027
r_lrange_other5.024
r_mcangle_it2.982
r_mcangle_other2.981
r_scangle_it2.928
r_scangle_other2.927
r_mcbond_it1.747
r_mcbond_other1.746
r_scbond_it1.693
r_scbond_other1.692
r_angle_refined_deg1.227
r_angle_other_deg1.112
r_nbd_refined0.189
r_nbd_other0.181
r_symmetry_nbd_other0.173
r_symmetry_nbd_refined0.173
r_nbtor_refined0.155
r_xyhbond_nbd_refined0.149
r_symmetry_xyhbond_nbd_refined0.143
r_symmetry_nbtor_other0.077
r_chiral_restr0.053
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5406
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing