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Apoflavodoxin from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FUE PDB ENTRY 1FUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.61 α = 90 b = 45.712 β = 90 c = 86.652 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 BRUCKER-NONIUS MONTEL MIRRORS 2004-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ROTATING ANODE
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 2.04 20.3 98.9 0.17 0.17 11.8 5.1 9402
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 2.11 2.18 90.4 0.56 0.56 1.3 1.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FUE 2.11 9 8016 625 100 0.206 0.2 0.2232 0.288 RANDOM 19.55
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] -0.49 0.09 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.729 r_scangle_it 3.077 r_scbond_it 1.977 r_angle_refined_deg 1.464 r_mcangle_it 1.177 r_angle_other_deg 0.829 r_mcbond_it 0.639 r_symmetry_vdw_refined 0.251 r_nbd_other 0.249 r_symmetry_hbond_refined 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.729 r_scangle_it 3.077 r_scbond_it 1.977 r_angle_refined_deg 1.464 r_mcangle_it 1.177 r_angle_other_deg 0.829 r_mcbond_it 0.639 r_symmetry_vdw_refined 0.251 r_nbd_other 0.249 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.218 r_symmetry_vdw_other 0.216 r_xyhbond_nbd_refined 0.192 r_nbtor_other 0.088 r_chiral_restr 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1228 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling MOLREP phasing