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Crystal structure of PH0822
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20% PEG8000, 0.01M imidazole, 0.01M adenosine-5-triphosphate disodium salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.95 37.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.932 α = 90 b = 99.877 β = 112.33 c = 48.812 γ = 90
Symmetry Space Group C 1 2 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 2006-10-29 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) 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 20 77.4 0.067 0.06 15.8657 2.75782 21963 -3 12.2
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 2 2.09 40.6 0.123 0.144 4.51497 1.5 1444
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1O13 2 20 20849 1084 77.28 0.21666 0.21419 0.2155 0.26242 0.2238 RANDOM 29.102
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] -0.01 0.12 0.53 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.245 r_dihedral_angle_3_deg 19.313 r_dihedral_angle_4_deg 18.185 r_dihedral_angle_1_deg 5.583 r_scangle_it 4.929 r_scbond_it 3.263 r_mcangle_it 2.172 r_angle_refined_deg 1.871 r_mcbond_it 1.385 r_nbtor_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.245 r_dihedral_angle_3_deg 19.313 r_dihedral_angle_4_deg 18.185 r_dihedral_angle_1_deg 5.583 r_scangle_it 4.929 r_scbond_it 3.263 r_mcangle_it 2.172 r_angle_refined_deg 1.871 r_mcbond_it 1.385 r_nbtor_refined 0.331 r_nbd_refined 0.252 r_symmetry_vdw_refined 0.247 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.137 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3529 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing