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2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O6Z PDB ENTRY 1O6Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 3UL OF PROTEIN PLUS 4UL OF MPD WERE EQUILIBRATED AGAINST 58% MPD VIA THE SITTING DROP REVERSE VAPOUR DIFFUSION TECHNIQUE, pH 7.00
Crystal Properties Matthews coefficient Solvent content 3.19 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.151 α = 90 b = 114.24 β = 93.48 c = 124.141 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD MIRRORS 2005-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 20 93.9 0.1 11.1 3.2 112033 12.851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 85.4 0.3 3 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1O6Z 2 20 112033 5643 93.8 0.2252 0.2252 0.2297 0.2701 RANDOM 21.3
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] -7.96 -0.158 1.841 6.118
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.38 c_scangle_it 4.11 c_mcangle_it 3.249 c_scbond_it 2.778 c_mcbond_it 2.091 c_angle_deg 1.52954 c_improper_angle_d 0.98 c_bond_d 0.012053 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.38 c_scangle_it 4.11 c_mcangle_it 3.249 c_scbond_it 2.778 c_mcbond_it 2.091 c_angle_deg 1.52954 c_improper_angle_d 0.98 c_bond_d 0.012053 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9052 Nucleic Acid Atoms Solvent Atoms 1023 Heterogen Atoms 8
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling