X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OD0PDB ENTRY 1OD0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1710MG/ML PROTEIN IN 15% PEG 4000, 0.2 M CAAC, 0.1 M IMIDAZOLE PH7, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.562α = 90
b = 94.595β = 90
c = 113.48γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDSAGITALLY FOCUSING GE(220) AND A MULTILAYER2003-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
124095.70.06121.65.2266518
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)
122.071000.4573.125.5

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 1OD0272.5563027327795.60.2070.2040.258RANDOM34
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]
-0.04-0.490.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.128
r_dihedral_angle_4_deg18.877
r_dihedral_angle_3_deg16.535
r_dihedral_angle_1_deg6.126
r_scangle_it2.926
r_scbond_it1.989
r_angle_refined_deg1.415
r_mcangle_it1.345
r_mcbond_it0.796
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.128
r_dihedral_angle_4_deg18.877
r_dihedral_angle_3_deg16.535
r_dihedral_angle_1_deg6.126
r_scangle_it2.926
r_scbond_it1.989
r_angle_refined_deg1.415
r_mcangle_it1.345
r_mcbond_it0.796
r_nbtor_refined0.315
r_nbd_refined0.207
r_symmetry_vdw_refined0.176
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.147
r_chiral_restr0.107
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms7196
Nucleic Acid Atoms
Solvent Atoms551
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling