2BP7

New crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6PROTEIN SAMPLE (1-5 PHOSPHATE PH6.3, 10MM DTT, 4MM MGCL2, 2MM ALPHA-CHLOROISOCAPROATE, 1MM THIAMINE DIPHOSPHATE., pH 5.60
Crystal Properties
Matthews coefficientSolvent content
3.3563

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.866α = 90
b = 156.866β = 90
c = 619.605γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002002-03-05MSINGLE 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
12.92089.60.06102.1101157
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)
12.93330.312.4

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 1QS02.92073031387076.50.2280.2270.254RANDOM35.72
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]
-0.24-0.12-0.240.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.943
r_dihedral_angle_4_deg17.498
r_dihedral_angle_3_deg15.179
r_dihedral_angle_1_deg4.685
r_mcangle_it3.169
r_scbond_it2.73
r_scangle_it2.701
r_mcbond_it1.937
r_angle_refined_deg0.961
r_symmetry_vdw_refined0.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.943
r_dihedral_angle_4_deg17.498
r_dihedral_angle_3_deg15.179
r_dihedral_angle_1_deg4.685
r_mcangle_it3.169
r_scbond_it2.73
r_scangle_it2.701
r_mcbond_it1.937
r_angle_refined_deg0.961
r_symmetry_vdw_refined0.355
r_nbtor_refined0.309
r_nbd_refined0.214
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.139
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms22980
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing