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Thermostable Penicillin G acylase from Alcaligenes faecalis in orthorhombic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GK9 PDB ENTRY 1GK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 303 15% PEG8000, 0.1M Tris-Hcl, pH7.5, 60uL of b-octyl- glucopyranoside (0.50% w/v), VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.4 48.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.929 α = 90 b = 86.016 β = 90 c = 260.181 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS IV Mirrors 2007-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.514
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 3.306 46.823 99.7 0.137 9.23 5.73 12626 12602 1 33.34
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 3.31 3.39 96.8 0.331 4.81 5.07 806
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 (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 1GK9 3.31 46.82 12647 11989 613 99.7 0.283 0.281 0.2724 0.315 0.3053 RANDOM 40.97
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] 0.02 0.04 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.744 r_dihedral_angle_3_deg 17.853 r_dihedral_angle_4_deg 11.682 r_dihedral_angle_1_deg 4.262 r_angle_refined_deg 0.875 r_mcangle_it 0.471 r_mcbond_it 0.267 r_scangle_it 0.128 r_scbond_it 0.072 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.744 r_dihedral_angle_3_deg 17.853 r_dihedral_angle_4_deg 11.682 r_dihedral_angle_1_deg 4.262 r_angle_refined_deg 0.875 r_mcangle_it 0.471 r_mcbond_it 0.267 r_scangle_it 0.128 r_scbond_it 0.072 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 6000 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing