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Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YPN PDB ENTRY 2YPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 PROTEIN WAS CRYSTALLISED AT PH 5.3 IN SITTING DROPS OF 0.05 ML WITH 6-7 MG/ML OF PROTEIN, 0.3 MM EDTA, 15 MM DITHIOTHREITOL, 10%(W/V) PEG6000 AND 0.01% NAN3 IN 0.1 M SODIUM ACETATE.
Crystal Properties Matthews coefficient Solvent content 2.45 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.5 α = 90 b = 75.9 β = 90 c = 50.1 γ = 90
Symmetry Space Group P 21 21 2
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 1997-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID09 ESRF ID09
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 1.66 43.85 87 34417
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 1.66 1.75 70.7
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 PDB ENTRY 2YPN 1.66 43.85 32708 1709 87 0.2 0.198 0.2104 0.247 0.2534 RANDOM
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_scangle_it 4.704 r_scbond_it 3.14 r_angle_other_deg 2.004 r_mcangle_it 1.982 r_mcbond_it 1.174 r_dihedral_angle_3_deg 0.98 r_symmetry_vdw_refined 0.304 r_symmetry_vdw_other 0.292 r_nbd_refined 0.281 r_symmetry_hbond_refined 0.262
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.704 r_scbond_it 3.14 r_angle_other_deg 2.004 r_mcangle_it 1.982 r_mcbond_it 1.174 r_dihedral_angle_3_deg 0.98 r_symmetry_vdw_refined 0.304 r_symmetry_vdw_other 0.292 r_nbd_refined 0.281 r_symmetry_hbond_refined 0.262 r_nbd_other 0.218 r_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_other 0.141 r_chiral_restr 0.117 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling O phasing