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Crystal Structure of Myoglobin with Charge Neutralized Heme, ZnDMb-dme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YMB 1YMB from PDB data base
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 12-17 mg/ml protein solution, 3.3 M ammonium sulfate, 0.1 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.604 α = 90 b = 30.577 β = 97.66 c = 56.485 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 MARMOSAIC 300 mm CCD 2006-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97934 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.14 55.99 99.5 0.084 6.7 8041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.14 2.203 96.8 0.187 5.4
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 1YMB from PDB data base 2.15 55.99 8041 373 99.05 0.17807 0.17538 0.1755 0.23191 0.2348 RANDOM 18.675
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] 1.12 -0.14 0.46 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.409 r_dihedral_angle_3_deg 17.489 r_dihedral_angle_4_deg 13.255 r_dihedral_angle_1_deg 5.373 r_angle_refined_deg 2.991 r_scangle_it 2.593 r_scbond_it 1.667 r_mcangle_it 1.172 r_mcbond_it 0.68 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.409 r_dihedral_angle_3_deg 17.489 r_dihedral_angle_4_deg 13.255 r_dihedral_angle_1_deg 5.373 r_angle_refined_deg 2.991 r_scangle_it 2.593 r_scbond_it 1.667 r_mcangle_it 1.172 r_mcbond_it 0.68 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1204 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing