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High resolution crystal structure of beta-porphyranase A from Zobellia galactanivorans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 293 18-20% PEG 4000, 0.2 M AMMONIUM SULFATE AND 0.1 M SODIUM ACETATE PH 4.6 AT 20 DEGREES C
Crystal Properties Matthews coefficient Solvent content 2.09 41.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.27 α = 90 b = 70.27 β = 90 c = 92.47 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 315r 2008-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.1 30.5 99.9 0.08 7.5 10.5 108086 0.01
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 1.1 1.16 99.9 0.12 4.2 10.5
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 MAD THROUGHOUT NONE 1.1 25.86 89663 4675 87.9 0.12495 0.1235 0.1271 0.15176 0.1541 RANDOM 11.897
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.062 r_dihedral_angle_4_deg 18.731 r_dihedral_angle_3_deg 11.515 r_dihedral_angle_1_deg 7.608 r_scangle_it 5.121 r_scbond_it 3.999 r_mcangle_it 2.719 r_rigid_bond_restr 2.426 r_angle_refined_deg 2.28 r_mcbond_it 2.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.062 r_dihedral_angle_4_deg 18.731 r_dihedral_angle_3_deg 11.515 r_dihedral_angle_1_deg 7.608 r_scangle_it 5.121 r_scbond_it 3.999 r_mcangle_it 2.719 r_rigid_bond_restr 2.426 r_angle_refined_deg 2.28 r_mcbond_it 2.033 r_chiral_restr 0.135 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2100 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXD phasing