X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MEOPDB entry 1MEO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529120% PEG 3350, 0.1 M Mg formate, 0.1 M NaI, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3246.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.273α = 90
b = 73.366β = 90
c = 77.246γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 325 mm CCD2007-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97900SSRLBL9-2

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
11.2552.2251000.06624.214.4115083
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)
1.251.321000.8223.614.1

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 REPLACEMENTTHROUGHOUTPDB entry 1MEO1.336.69112329102250512999.530.164870.163740.18602RANDOM12.078
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]
0.16-0.1-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.496
r_dihedral_angle_4_deg14.491
r_dihedral_angle_3_deg10.863
r_dihedral_angle_1_deg5.584
r_sphericity_free4.353
r_sphericity_bonded4.135
r_scangle_it3.625
r_scbond_it2.409
r_mcangle_it1.843
r_angle_refined_deg1.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.496
r_dihedral_angle_4_deg14.491
r_dihedral_angle_3_deg10.863
r_dihedral_angle_1_deg5.584
r_sphericity_free4.353
r_sphericity_bonded4.135
r_scangle_it3.625
r_scbond_it2.409
r_mcangle_it1.843
r_angle_refined_deg1.335
r_rigid_bond_restr1.17
r_mcbond_it1.115
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3045
Nucleic Acid Atoms
Solvent Atoms449
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement