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Crystal structure of GTP cyclohydrolase II from Helicobacter pylori 26695
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M ammonium citrate tribasic, 15% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.283 α = 90 b = 69.283 β = 90 c = 179.763 γ = 90
Symmetry Space Group P 41 21 2
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 MAR scanner 345 mm plate 2012-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.199 64.65 96.2 0.071 33.1 8.8 23212 -3 -3 38.7
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 2.199 2.24 72.3 0.281 2.3 2.3 831
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 (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 2BZ0 2.199 64.65 21061 1131 95.92 0.2116 0.2139 0.21158 0.2189 0.26048 0.2636 RANDOM 47.243
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 1.68 -3.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.748 r_dihedral_angle_4_deg 16.439 r_dihedral_angle_3_deg 14.876 r_long_range_B_refined 7.693 r_long_range_B_other 7.655 r_dihedral_angle_1_deg 6.368 r_scangle_other 4.957 r_mcangle_it 4.166 r_mcangle_other 4.165 r_scbond_it 3.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.748 r_dihedral_angle_4_deg 16.439 r_dihedral_angle_3_deg 14.876 r_long_range_B_refined 7.693 r_long_range_B_other 7.655 r_dihedral_angle_1_deg 6.368 r_scangle_other 4.957 r_mcangle_it 4.166 r_mcangle_other 4.165 r_scbond_it 3.095 r_scbond_other 3.072 r_mcbond_other 2.539 r_mcbond_it 2.538 r_angle_refined_deg 1.237 r_angle_other_deg 0.728 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2672 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 18
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling