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Crystal structure of PH1346 protein from Pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QDL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.8 295 Acetate, PEG, pH 4.8, microbatch, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.3 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.808 α = 90 b = 63.48 β = 90 c = 65.161 γ = 90
Symmetry Space Group P 21 21 21
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 RH COATED BENT-CYLINDRICAL MIRROR 2004-03-21 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 1.45 40 99.9 0.07 14.7 7 33392 33220 10.81
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) 1.45 1.5 100 0.25
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1QDL 1.45 28.99 33392 33220 1758 99.83 0.15638 0.15638 0.15544 0.17365 0.1674 RANDOM 9.924
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] 0.88 -0.21 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.637 r_scangle_it 4.032 r_scbond_it 2.457 r_mcangle_it 1.571 r_angle_refined_deg 1.481 r_angle_other_deg 0.856 r_mcbond_it 0.815 r_symmetry_vdw_other 0.282 r_nbd_refined 0.278 r_nbd_other 0.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.637 r_scangle_it 4.032 r_scbond_it 2.457 r_mcangle_it 1.571 r_angle_refined_deg 1.481 r_angle_other_deg 0.856 r_mcbond_it 0.815 r_symmetry_vdw_other 0.282 r_nbd_refined 0.278 r_nbd_other 0.256 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.126 r_nbtor_other 0.092 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.009 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1504 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing