X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R5VPDB ENTRY 2R5V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.51 MICROLITRE 10 MG ML-1 HMS VARIANT, PREINCUBATED WITH 1.25 MM COCL2 AND 2.5 MM R-MANDELATE) PLUS 1 MICROLITRE MOTHER LIQUOR. THE BEST CRYSTALS WERE ROUTINELY OBTAINED IN CRYSTAL DROPS CONTAINING 0.05 M TRIS/CL PH 9.0, 0.1 M MGCL2, 7.5% (W/V) PEG 4K AND 2.5% (V/V) 2-METHYL-1,4-PENTANEDIOL.
Crystal Properties
Matthews coefficientSolvent content
2.5452

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.87α = 90
b = 122.87β = 90
c = 54.86γ = 90
Symmetry
Space GroupP 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCD2012-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.9561.441000.0615.66.7570142
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)
11.952.011000.493.96.9

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 2R5V1.9554.9557014304999.970.177110.175050.21504RANDOM34.805
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]
-0.68-0.681.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.114
r_dihedral_angle_4_deg18.129
r_dihedral_angle_3_deg14.576
r_dihedral_angle_1_deg6.715
r_mcangle_it4.683
r_scbond_it4.594
r_mcbond_it3.494
r_angle_refined_deg2.002
r_chiral_restr0.156
r_bond_refined_d0.021
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.114
r_dihedral_angle_4_deg18.129
r_dihedral_angle_3_deg14.576
r_dihedral_angle_1_deg6.715
r_mcangle_it4.683
r_scbond_it4.594
r_mcbond_it3.494
r_angle_refined_deg2.002
r_chiral_restr0.156
r_bond_refined_d0.021
r_gen_planes_refined0.012
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
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms5051
Nucleic Acid Atoms
Solvent Atoms531
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing