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Crystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 PEG 6000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.8 67.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.028 α = 90 b = 115.028 β = 90 c = 437.057 γ = 120
Symmetry Space Group P 61 2 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 RIGAKU RAXIS V 2002-04-12 M MAD 2 1 x-ray 100 CCD ADSC QUANTUM 315 2004-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 0.9794, 0.97925, 1.02 SPring-8 BL45PX 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 30 92.3 81242
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.2 29.36 77169 4073 92.3 0.20514 0.20315 0.24262 0.2236 RANDOM 35.145
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.195 r_dihedral_angle_4_deg 22.332 r_dihedral_angle_3_deg 20.145 r_dihedral_angle_1_deg 7.495 r_scangle_it 3.683 r_scbond_it 2.366 r_angle_refined_deg 1.73 r_mcangle_it 1.503 r_mcbond_it 0.888 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.195 r_dihedral_angle_4_deg 22.332 r_dihedral_angle_3_deg 20.145 r_dihedral_angle_1_deg 7.495 r_scangle_it 3.683 r_scbond_it 2.366 r_angle_refined_deg 1.73 r_mcangle_it 1.503 r_mcbond_it 0.888 r_nbtor_refined 0.313 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.215 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.139 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 7802 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing