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2.25 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui after second radiation burn (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 3.45 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.377 α = 90 b = 114.574 β = 93.34 c = 124.529 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 2.25 20 96.2 0.11 11.1 3.3 81346 15.716
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 2.25 2.37 90.8 0.33 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 2.25 20 81346 4084 96.1 0.2199 0.2199 0.2212 0.271 RANDOM 24.3193
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] -9.1 -0.194 1.712 7.388
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.31 c_scangle_it 4.367 c_scbond_it 3.205 c_mcangle_it 2.826 c_mcbond_it 1.958 c_angle_deg 1.43407 c_improper_angle_d 0.92 c_bond_d 0.01013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.31 c_scangle_it 4.367 c_scbond_it 3.205 c_mcangle_it 2.826 c_mcbond_it 1.958 c_angle_deg 1.43407 c_improper_angle_d 0.92 c_bond_d 0.01013 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 9051 Nucleic Acid Atoms Solvent Atoms 1023 Heterogen Atoms 8
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling