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Carbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [30 min]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MBC PDB ENTRY 1MBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 6 293 2.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 34.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.425 α = 90 b = 30.72 β = 105.54 c = 63.843 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MAR CCD 165 mm 2007-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW14A 0.827 Photon Factory AR-NW14A
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 1.21 50 98.1 0.052 13.2 3.6 38789 -3
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) 1.21 1.25 85.5 0.256 3 3318
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 PDB ENTRY 1MBC 1.21 15.66 38771 1945 98.61 0.145 0.143 0.141 0.182 0.1791 RANDOM 14.571
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] 0.03 -0.01 0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.881 r_dihedral_angle_4_deg 18.099 r_dihedral_angle_3_deg 14.069 r_sphericity_free 9.609 r_scangle_it 5.574 r_sphericity_bonded 5.368 r_dihedral_angle_1_deg 4.878 r_scbond_it 4.152 r_mcangle_it 2.868 r_rigid_bond_restr 2.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.881 r_dihedral_angle_4_deg 18.099 r_dihedral_angle_3_deg 14.069 r_sphericity_free 9.609 r_scangle_it 5.574 r_sphericity_bonded 5.368 r_dihedral_angle_1_deg 4.878 r_scbond_it 4.152 r_mcangle_it 2.868 r_rigid_bond_restr 2.659 r_mcbond_it 2.003 r_angle_refined_deg 1.787 r_metal_ion_refined 0.597 r_nbtor_refined 0.319 r_nbd_refined 0.308 r_symmetry_hbond_refined 0.144 r_symmetry_vdw_refined 0.143 r_chiral_restr 0.131 r_xyhbond_nbd_refined 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1217 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling