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Crystal structure of porphyranase A (PorA) in complex with neo-porphyrotetraose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 PEG 4000, Ammoniumsulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.09 α = 90 b = 68.378 β = 90 c = 71.268 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 2009-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 49.34 94.6 0.062 0.057 20.8 6.7 27062 27062 1 1 11.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 91.4 0.212 0.195 8.4 6.2 3741
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 49.34 1 27062 25651 1381 93.95 0.15965 0.15965 0.15718 0.20461 0.1962 RANDOM 13.339
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] 0.22 -0.19 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_3_deg 13.79 r_dihedral_angle_4_deg 11.31 r_dihedral_angle_1_deg 7.772 r_scangle_it 4.909 r_scbond_it 3.162 r_angle_refined_deg 2.302 r_mcangle_it 2.076 r_mcbond_it 1.266 r_chiral_restr 0.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_3_deg 13.79 r_dihedral_angle_4_deg 11.31 r_dihedral_angle_1_deg 7.772 r_scangle_it 4.909 r_scbond_it 3.162 r_angle_refined_deg 2.302 r_mcangle_it 2.076 r_mcbond_it 1.266 r_chiral_restr 0.374 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2109 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 73
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling