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Crystal structure of a putative extracellular heme-binding protein (DESPIG_02683) from Desulfovibrio piger ATCC 29098 at 1.24 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 2.4M ammonium sulfate, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.9 35.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.964 α = 90 b = 80.964 β = 90 c = 72.927 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-05-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97879,0.97812 SSRL BL11-1
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 1.24 28.625 96.3 0.033 14.7 131689 -3 11.502
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 1.24 1.28 92.2 0.539 1.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.24 28.625 131689 6635 99.24 0.1291 0.128 0.1308 0.1494 0.1504 RANDOM 17.4296
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] -0.14 -0.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.263 r_dihedral_angle_4_deg 18.737 r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 5.325 r_scangle_it 4.693 r_sphericity_free 3.999 r_scbond_it 3.093 r_sphericity_bonded 2.384 r_mcangle_it 2.342 r_mcbond_it 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.263 r_dihedral_angle_4_deg 18.737 r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 5.325 r_scangle_it 4.693 r_sphericity_free 3.999 r_scbond_it 3.093 r_sphericity_bonded 2.384 r_mcangle_it 2.342 r_mcbond_it 1.52 r_angle_refined_deg 1.23 r_rigid_bond_restr 1.116 r_mcbond_other 0.892 r_angle_other_deg 0.868 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4140 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 57
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SOLVE phasing XSCALE data scaling REFMAC refinement XDS data reduction