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Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.3 295 MES-NaOH, PEG 4000, pH 6.3, microbatch, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.3 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.12 α = 90 b = 66.12 β = 90 c = 125.072 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU Graphite 2005-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.9 SPring-8 BL26B1
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 1.65 40 100 0.066 7.1 5.6 73383 73383 21.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 100
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 (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 1VGG 1.65 33.7 73383 73383 3748 100 0.185 0.185 0.1863 0.204 0.2012 RANDOM 26.9
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] 5.85 3.62 5.85 -11.7
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 2.83 c_scbond_it 1.87 c_angle_deg 1.4 c_mcangle_it 1.37 c_improper_angle_d 0.96 c_mcbond_it 0.94 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4948 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 28
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing