X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NAYPDB ENTRY 1NAY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
179 MM POTASSIUM PHOSPHATE, PH 7.0, 10% D2O
Crystal Properties
Matthews coefficientSolvent content
2.2141.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 29.83α = 90
b = 29.83β = 90
c = 75.08γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
10.982099.20.0510.42.342623-37.139
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)
10.981.0398.40.282.82.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NAY0.9817.9841289130099.230.129790.129220.1471RANDOM7.614
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]
0.420.210.42-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.669
r_dihedral_angle_3_deg8.64
r_dihedral_angle_4_deg7.854
r_dihedral_angle_1_deg5.682
r_scangle_it2.541
r_mcangle_it2.113
r_scbond_it1.676
r_mcbond_it1.417
r_angle_refined_deg1.246
r_angle_other_deg0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.669
r_dihedral_angle_3_deg8.64
r_dihedral_angle_4_deg7.854
r_dihedral_angle_1_deg5.682
r_scangle_it2.541
r_mcangle_it2.113
r_scbond_it1.676
r_mcbond_it1.417
r_angle_refined_deg1.246
r_angle_other_deg0.82
r_rigid_bond_restr0.702
r_mcbond_other0.331
r_chiral_restr0.101
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms669
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing