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Carbonmonoxy Sperm Whale Myoglobin at 100 K: Laser on [450 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 1.88 34.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.342 α = 90 b = 30.635 β = 105.36 c = 63.714 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 100 CCD MAR CCD 165 mm 2008-02-20 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 88.4 0.052 10.4 3.5 34942 -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 36.6 0.408 2 1422
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 19.94 34930 1730 88.78 0.154 0.152 0.1512 0.212 0.2114 RANDOM 15.605
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] 0.02 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.176 r_dihedral_angle_4_deg 14.137 r_dihedral_angle_3_deg 13.539 r_sphericity_free 10.759 r_scangle_it 6.666 r_sphericity_bonded 6.275 r_dihedral_angle_1_deg 5.301 r_scbond_it 4.851 r_mcangle_it 3.527 r_rigid_bond_restr 3.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.176 r_dihedral_angle_4_deg 14.137 r_dihedral_angle_3_deg 13.539 r_sphericity_free 10.759 r_scangle_it 6.666 r_sphericity_bonded 6.275 r_dihedral_angle_1_deg 5.301 r_scbond_it 4.851 r_mcangle_it 3.527 r_rigid_bond_restr 3.159 r_mcbond_it 2.529 r_angle_refined_deg 2.208 r_nbtor_refined 0.32 r_nbd_refined 0.302 r_metal_ion_refined 0.255 r_symmetry_vdw_refined 0.206 r_chiral_restr 0.163 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.129 r_bond_refined_d 0.024 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1217 Nucleic Acid Atoms Solvent Atoms 158 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