X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H6TPDB ENTRY 1H6T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29320 DEG C IN HANGING OR SITTING-DROPS WITH 1.5 UL PROTEIN (5 MG/ML) PLUS 1.5 UL RESERVOIR (0.1 M MES, PH 5.5, 14 % MPD) MICROSEEDED FROM A SIMILAR CONDITION (0.1 M MES PH 6.0, 6.5 % PEG6000 AND 5 MM ZNCL2).
Crystal Properties
Matthews coefficientSolvent content
6.1680

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.4α = 90
b = 126.4β = 90
c = 107.86γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
13.21598.70.1318.314.716581-386
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)
13.23.281000.552.9

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 1H6T3.214.97157528291000.198470.197130.22475RANDOM73.16
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]
4.692.354.69-7.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.273
r_dihedral_angle_3_deg19.934
r_dihedral_angle_4_deg10.471
r_dihedral_angle_1_deg8.955
r_scangle_it3.514
r_angle_refined_deg2.037
r_scbond_it1.973
r_mcangle_it1.242
r_angle_other_deg1.134
r_mcbond_it0.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.273
r_dihedral_angle_3_deg19.934
r_dihedral_angle_4_deg10.471
r_dihedral_angle_1_deg8.955
r_scangle_it3.514
r_angle_refined_deg2.037
r_scbond_it1.973
r_mcangle_it1.242
r_angle_other_deg1.134
r_mcbond_it0.631
r_mcbond_other0.101
r_chiral_restr0.1
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2271
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing