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Nitromethane Modified Horse Heart Myoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NPG PDB entry 1NPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 295 Ammonium Sulfate, Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.77 32.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.344 α = 90 b = 28.74 β = 106 c = 63.471 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2003-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54180
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 1.9 21.9 100 0.072 16.3 3.53 9380 9374 1 29.1
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) 1.9 1.947 66.62 0.266 4 2.81 974
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1NPG 1.9 19.93 1 9374 8787 444 94.48 0.16 0.16298 0.15969 0.1641 0.23119 0.1327 RANDOM 18.193
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 r_dihedral_angle_2_deg 38.739 r_dihedral_angle_4_deg 18.364 r_dihedral_angle_3_deg 14.149 r_dihedral_angle_1_deg 5.448 r_scangle_it 3.795 r_scbond_it 2.545 r_angle_refined_deg 1.501 r_mcangle_it 1.379 r_mcbond_it 0.884 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.739 r_dihedral_angle_4_deg 18.364 r_dihedral_angle_3_deg 14.149 r_dihedral_angle_1_deg 5.448 r_scangle_it 3.795 r_scbond_it 2.545 r_angle_refined_deg 1.501 r_mcangle_it 1.379 r_mcbond_it 0.884 r_nbtor_refined 0.295 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.206 r_xyhbond_nbd_refined 0.192 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.101 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 1194 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling MOLREP phasing