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Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ARZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 0.2M Magnesium Acetate, 0.1M Hepes, 23% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.19 61.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.1 α = 90 b = 62.1 β = 90 c = 301.406 γ = 120
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 210r 2015-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.25 43.77 99.9 0.097 0.046 0.996 14.1 5.2 31095
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 99.2 0.637 0.417 0.516 1.9 3.2 2816
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ARZ 2.25 43.77 29399 1588 99.88 0.1869 0.1846 0.1901 0.2298 0.2359 RANDOM 33.206
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] -0.34 -0.17 -0.34 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.04 r_dihedral_angle_4_deg 20.378 r_dihedral_angle_3_deg 14.473 r_dihedral_angle_1_deg 6.262 r_mcangle_it 3.736 r_mcbond_it 2.474 r_mcbond_other 2.469 r_angle_refined_deg 1.766 r_angle_other_deg 1.133 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.04 r_dihedral_angle_4_deg 20.378 r_dihedral_angle_3_deg 14.473 r_dihedral_angle_1_deg 6.262 r_mcangle_it 3.736 r_mcbond_it 2.474 r_mcbond_other 2.469 r_angle_refined_deg 1.766 r_angle_other_deg 1.133 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3622 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing