X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MJCPDB ENTRY 3MJC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172932.5 M DL-malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.439α = 72.77
b = 63.71β = 67.09
c = 71.824γ = 89.79
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.462.6894.80.04424.32176916215.8
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)
11.41.4291.70.4522

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 3MJC1.462.6888681176916886594.80.20.1990.226RANDOM18.09
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]
0.350.3-0.22-0.34-0.680.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.699
r_dihedral_angle_4_deg18.954
r_dihedral_angle_3_deg15.491
r_dihedral_angle_1_deg6.076
r_scangle_it5.576
r_scbond_it3.665
r_angle_refined_deg2.669
r_mcangle_it2.427
r_mcbond_it1.524
r_chiral_restr0.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.699
r_dihedral_angle_4_deg18.954
r_dihedral_angle_3_deg15.491
r_dihedral_angle_1_deg6.076
r_scangle_it5.576
r_scbond_it3.665
r_angle_refined_deg2.669
r_mcangle_it2.427
r_mcbond_it1.524
r_chiral_restr0.265
r_bond_refined_d0.031
r_gen_planes_refined0.016
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6924
Nucleic Acid Atoms
Solvent Atoms504
Heterogen Atoms144

Software

Software
Software NamePurpose
ADSCdata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling