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Crystal structure of hypothetical protein of HP0062 from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GTS PDB Entry 2GTS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 5% PEG 3350, 100mM citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.83 32.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.303 α = 90 b = 51.895 β = 90 c = 83.305 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 CCD ADSC QUANTUM 210 2006-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.23985 PAL/PLS 6C1
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 97.1 0.049 59.33 12.8 20637 1 1
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) 1.65 1.71 95.1 0.248 10.97 12.6
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 PDB Entry 2GTS 1.65 40 20571 19518 1053 97.17 0.18828 0.18636 0.1931 0.22512 0.2287 RANDOM 15.303
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] -0.69 1.09 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.566 r_dihedral_angle_4_deg 16.799 r_dihedral_angle_3_deg 14.017 r_scangle_it 4.589 r_dihedral_angle_1_deg 3.957 r_scbond_it 3.047 r_mcangle_it 1.835 r_mcbond_it 1.173 r_angle_refined_deg 1.125 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.566 r_dihedral_angle_4_deg 16.799 r_dihedral_angle_3_deg 14.017 r_scangle_it 4.589 r_dihedral_angle_1_deg 3.957 r_scbond_it 3.047 r_mcangle_it 1.835 r_mcbond_it 1.173 r_angle_refined_deg 1.125 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.114 r_symmetry_hbond_refined 0.092 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 1554 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling