X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OKUPDB ENTRY 1OKU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.822% PEG 3350, 0.1M NA3-CIT, pH 7.80
Crystal Properties
Matthews coefficientSolvent content
2.3848.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.539α = 90
b = 113.139β = 90
c = 157.216γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2002-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.120930.1111.92.1701681
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)
12.12.21870.363.5

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 1OKU2.11569366215891.70.1780.1750.259RANDOM26.59
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]
-1.02-1.072.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.153
r_scangle_it8.443
r_dihedral_angle_1_deg8.028
r_scbond_it5.512
r_mcangle_it3.744
r_mcbond_it2.291
r_angle_refined_deg1.822
r_angle_other_deg0.896
r_symmetry_hbond_refined0.407
r_symmetry_vdw_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.153
r_scangle_it8.443
r_dihedral_angle_1_deg8.028
r_scbond_it5.512
r_mcangle_it3.744
r_mcbond_it2.291
r_angle_refined_deg1.822
r_angle_other_deg0.896
r_symmetry_hbond_refined0.407
r_symmetry_vdw_refined0.333
r_nbd_refined0.322
r_xyhbond_nbd_refined0.293
r_nbd_other0.271
r_symmetry_vdw_other0.254
r_chiral_restr0.119
r_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_gen_planes_other0.004
r_bond_other_d
r_dihedral_angle_2_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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8924
Nucleic Acid Atoms
Solvent Atoms935
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing