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Carbonmonoxy Sperm Whale Myoglobin at 140 K: Laser on [300 min]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 1.87 34.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.371 α = 90 b = 30.614 β = 105.79 c = 63.809 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 140 CCD MAR CCD 165 mm 2008-02-21 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 83.5 0.053 8.5 3.3 33117 -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 23.9 0.651 1.4 937
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 1MBC 1.21 17.02 33070 1642 84.49 0.161 0.158 0.1574 0.217 0.2172 RANDOM 16.194
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] -0.01 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.97 r_dihedral_angle_4_deg 24.819 r_dihedral_angle_3_deg 14.18 r_sphericity_free 13.24 r_scangle_it 7.719 r_sphericity_bonded 7.102 r_scbond_it 5.633 r_dihedral_angle_1_deg 5.509 r_mcangle_it 4.025 r_rigid_bond_restr 3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.97 r_dihedral_angle_4_deg 24.819 r_dihedral_angle_3_deg 14.18 r_sphericity_free 13.24 r_scangle_it 7.719 r_sphericity_bonded 7.102 r_scbond_it 5.633 r_dihedral_angle_1_deg 5.509 r_mcangle_it 4.025 r_rigid_bond_restr 3.67 r_mcbond_it 2.968 r_angle_refined_deg 2.661 r_metal_ion_refined 0.483 r_nbtor_refined 0.33 r_nbd_refined 0.309 r_symmetry_vdw_refined 0.252 r_chiral_restr 0.202 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.146 r_bond_refined_d 0.032 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1217 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling