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1.8 A resolution structure of the malate dehydrogenase from Picrophilus torridus in its apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other ONE POLY-ALA MONOMER OF OUR PREVIOUS SIRAS PTMALDH MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.5 293 9-14 % PEG 4000, 0.1 M CITRIC ACID PH 3.5, 293 K, 12-15 DAYS
Crystal Properties Matthews coefficient Solvent content 2.31 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.167 α = 90 b = 81.167 β = 90 c = 395.99 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 QUANTUM 315r TWO MIRRORS 2010-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.81 46.47 99.8 0.12 6.3 11.5 121716 -3 15.43
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 1.81 1.91 98.5 0.67 1.3 10.8
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 ONE POLY-ALA MONOMER OF OUR PREVIOUS SIRAS PTMALDH MODEL 1.811 46.473 1.34 121529 6078 99.78 0.1483 0.1464 0.1483 0.1848 0.1856 17.95
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.003 f_angle_d 1.096 f_chiral_restr 0.077 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9880 Nucleic Acid Atoms Solvent Atoms 1219 Heterogen Atoms 100
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHASER phasing PHENIX refinement