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Crystal Structure of the PH0510 protein from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J5X PDB ENTRY 1J5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.8 295 PEG 3350, lithium acetate, pH 7.8, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.15 42.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.228 α = 90 b = 79.485 β = 105.15 c = 67.497 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU JUPITER 210 2005-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.800 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 1.7 30 99.9 0.091 0.082 6.9 4.4 68213 68213 15.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 99.6 0.344 0.301 2.81 4.2 6735
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 PDB ENTRY 1J5X 1.7 30 68190 68190 3427 99.5 0.167 0.166 0.166 0.1685 0.189 0.1692 RANDOM 16.5
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] 1.3 -0.05 -1.47 0.17
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.81 c_scbond_it 1.9 c_mcangle_it 1.35 c_angle_deg 1.3 c_mcbond_it 0.95 c_improper_angle_d 0.89 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.81 c_scbond_it 1.9 c_mcangle_it 1.35 c_angle_deg 1.3 c_mcbond_it 0.95 c_improper_angle_d 0.89 c_bond_d 0.005 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 5190 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 13
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing