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Crystal structure of inosine-5'-monophosphate dehydrogenase from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZFJ 1ZFJ.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 9.6 291 50 %(v/v) PEG-200 CHES, pH 9.6, MICROBATCH, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.666 α = 90 b = 123.666 β = 90 c = 130.053 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS V 2004-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 30 100 0.116 0.11 9.9 7.3 56527 56527 33.473
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 2.1 2.18 100 0.618 4.09 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZFJ.pdb 2.1 29.23 56526 56526 2790 99.7 0.206 0.206 0.205 0.1995 0.228 0.2242 RANDOM 40.3
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] -6.7 -6.7 13.41
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5398 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling MOLREP phasing CNS refinement HKL-2000 data reduction