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Crystal structure of PcyA V225D-biliverdin IX alpha complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 0.8-1.0M NaH2PO4, 1.0-1.2M K2HPO4, 100mM sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.046 α = 90 b = 74.875 β = 90 c = 84.169 γ = 90
Symmetry Space Group P 21 21 21
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 2009-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 50 98.5 0.08 16.9 6.8 36692 36692
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 1.97 99.6 0.37 6.7 3623
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2D1E 1.9 32.88 34843 34843 1842 98.31 0.2316 0.23403 0.23081 0.2454 0.29483 0.3063 RANDOM 36.837
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] -0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.707 r_dihedral_angle_3_deg 18.492 r_dihedral_angle_4_deg 17.672 r_dihedral_angle_1_deg 7.829 r_scangle_it 4.23 r_scbond_it 2.868 r_angle_refined_deg 2.281 r_mcangle_it 2.045 r_mcbond_it 1.346 r_angle_other_deg 0.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.707 r_dihedral_angle_3_deg 18.492 r_dihedral_angle_4_deg 17.672 r_dihedral_angle_1_deg 7.829 r_scangle_it 4.23 r_scbond_it 2.868 r_angle_refined_deg 2.281 r_mcangle_it 2.045 r_mcbond_it 1.346 r_angle_other_deg 0.672 r_symmetry_vdw_refined 0.352 r_nbtor_refined 0.312 r_nbtor_other 0.289 r_nbd_other 0.258 r_nbd_refined 0.24 r_mcbond_other 0.194 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.172 r_chiral_restr 0.137 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3810 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement