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L89S Mutant of FeBMb Sperm Whale Myoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.57 277.15 Crystals of L89S-FeBMb were set up and grown at 4 C on hanging drops containing 0.1M MES pH 6.57, 0.2M NaOAC.3H2O, 30% PEG 6K as well buffer. Drops contained an equal volume of 1 mM L89S-FeBMb in 20 mM TRIS.H2SO4 pH 8 and the well buffer. Prior to mounting, the
L89S-FeBMb crystals were soaked in buffer containing 0.1M MES pH 6.0, 0.2M NaOAC.3H2O, 30% PEG 6K for 30 min and then frozen in a cryoprotectant solution of 50 mM MES pH 6.0, and 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.359 α = 90 b = 48.075 β = 90 c = 78.237 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 ADSC QUANTUM 315 2015-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.83, 1.8 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.78 50 99.1 0.053 0.059 0.026 18.5 4.7 14785 23.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.81 86 0.241 0.271 0.121 0.95 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3M38 1.779 35.16 1.35 14741 1473 99.51 0.1682 0.164 0.1668 0.2053 0.2037 25.6569
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.01 f_angle_d 0.91 f_chiral_restr 0.044 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1218 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction PDB_EXTRACT data extraction HKL-2000 data scaling PHENIX phasing