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2.9 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HLP PDB ENTRY 2HLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 INITIAL PROTEIN DROPLET: 16 MG/ML PROTEIN, 10 MM NADH, 20 M RESERVOIR: 1.6 M AMMONIUM SULPHATE, 20% (V/V) GLYCEROL, 80 M DROPLET: EQUAL VOLUMES OF INITIAL PROTEIN DROPLET AND RESERVOIR WERE MIXED., pH 4.0
Crystal Properties Matthews coefficient Solvent content 3.6 62.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.964 α = 90 b = 112.964 β = 90 c = 71.294 γ = 90
Symmetry Space Group P 41 21 2
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 TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.91 59.76 83.6 0.05 26.9 8.7 8949 0.5 62.26
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 2.91 3.01 45.4 0.1 9.7 3.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2HLP 2.91 56.48 2.17 8932 492 84.26 0.1557 0.1519 0.1552 0.2186 0.2186 62.89
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] -10.0474 -10.0474 20.0947
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.859 f_angle_d 1.461 f_chiral_restr 0.124 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2237 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XDS data reduction BIOMOL data scaling AMoRE phasing