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Crystal Structure of PH0347 protein from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 9 295 Sodium chloride, Bicine, PEG-MME 550, pH 9.0, microbatch, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.511 α = 90 b = 101.166 β = 119.78 c = 78.646 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 IMAGE PLATE RIGAKU RAXIS 2005-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 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 2.6 50 99.7 0.057 9 3.6 32523 32607 46.1
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 2.6 2.69 98.8
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 1XX7 2.6 40 32607 32523 1616 99.66 0.195 0.195 0.195 0.1941 0.22531 0.2188 RANDOM 39.287
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] -1.68 -0.69 3.74 -2.75
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.83 r_scbond_it 3.511 r_mcangle_it 2.036 r_dihedral_angle_1_deg 1.973 r_angle_refined_deg 1.542 r_mcbond_it 1.022 r_symmetry_vdw_refined 0.332 r_nbd_refined 0.253 r_symmetry_hbond_refined 0.236 r_xyhbond_nbd_refined 0.193
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.83 r_scbond_it 3.511 r_mcangle_it 2.036 r_dihedral_angle_1_deg 1.973 r_angle_refined_deg 1.542 r_mcbond_it 1.022 r_symmetry_vdw_refined 0.332 r_nbd_refined 0.253 r_symmetry_hbond_refined 0.236 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.1 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8448 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling EPMR phasing