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The 1.58A Crystal Structure of Human Coproporphyrinogen Oxidase Reveals the Structural Basis of Hereditary Coproporphyria
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 MPD, citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.741 α = 90 b = 112.741 β = 90 c = 112.741 γ = 90
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 ADSC QUANTUM 315 2003-12-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9537, 0.9795, 0.9796 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 100 65081 65081 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.62 99.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 1.58 31.31 65081 61787 3294 99.47 0.18709 0.18598 0.1968 0.20755 0.1962 RANDOM 28.411
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 36.943 r_dihedral_angle_4_deg 14.636 r_dihedral_angle_3_deg 13.646 r_dihedral_angle_1_deg 5.968 r_scangle_it 2.56 r_mcangle_it 2.268 r_mcbond_it 2.115 r_scbond_it 2.023 r_angle_refined_deg 1.351 r_angle_other_deg 0.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.943 r_dihedral_angle_4_deg 14.636 r_dihedral_angle_3_deg 13.646 r_dihedral_angle_1_deg 5.968 r_scangle_it 2.56 r_mcangle_it 2.268 r_mcbond_it 2.115 r_scbond_it 2.023 r_angle_refined_deg 1.351 r_angle_other_deg 0.768 r_mcbond_other 0.344 r_symmetry_vdw_other 0.246 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.208 r_nbd_other 0.199 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.132 r_nbtor_other 0.086 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2702 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHARP phasing