2PWZ

Crystal structure of the apo form of E.Coli malate dehydrogenase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527720% (W/V) PEG 10000, 100 mM SODIUM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4750.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.466α = 90
b = 52.485β = 102.28
c = 170.2γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDdouble crystal Si(III) monochromator with horizontal saggital focusing system, Rh coated mirror for vertical focusing2007-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.283SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.25097.60.1210.1214.63.5632866328626.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3292.50.4110.4111.53.28651

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1IE32.2506328663286321197.60.2010.2010.1990.246RANDOM20.223
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]
-1.690.040.711
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.502
r_dihedral_angle_4_deg18.967
r_dihedral_angle_3_deg16.309
r_dihedral_angle_1_deg5.92
r_scangle_it3.451
r_scbond_it2.162
r_angle_refined_deg1.493
r_mcangle_it1.287
r_mcbond_it0.782
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.502
r_dihedral_angle_4_deg18.967
r_dihedral_angle_3_deg16.309
r_dihedral_angle_1_deg5.92
r_scangle_it3.451
r_scbond_it2.162
r_angle_refined_deg1.493
r_mcangle_it1.287
r_mcbond_it0.782
r_nbtor_refined0.297
r_symmetry_vdw_refined0.209
r_nbd_refined0.205
r_symmetry_hbond_refined0.182
r_xyhbond_nbd_refined0.149
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9060
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
MOLREPphasing