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Crystal structure of an enzyme from Penicillium herquei in condition1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C5O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 33% PEG4000, 0.1 M tri-sodium citrate pH 5.6, 2% iso-propanol
Crystal Properties Matthews coefficient Solvent content 2.09 41.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.574 α = 90 b = 55.104 β = 98.88 c = 70.972 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX-300 2018-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.33 25 96.4 0.072 0.077 0.026 7.3 8.2 117386
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.38 87.5 0.414 0.453 0.182 0.897 5.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3C5O 1.33 24.5 115313 2032 96.34 0.1864 0.18586 0.21491 0.2259 RANDOM 19.113
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] 0.19 0.03 -0.02 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.208 r_dihedral_angle_3_deg 12.392 r_dihedral_angle_4_deg 8.958 r_dihedral_angle_1_deg 7.539 r_long_range_B_refined 7.193 r_scbond_it 3.199 r_mcangle_it 2.203 r_angle_refined_deg 1.85 r_mcbond_it 1.448 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.208 r_dihedral_angle_3_deg 12.392 r_dihedral_angle_4_deg 8.958 r_dihedral_angle_1_deg 7.539 r_long_range_B_refined 7.193 r_scbond_it 3.199 r_mcangle_it 2.203 r_angle_refined_deg 1.85 r_mcbond_it 1.448 r_chiral_restr 0.122 r_bond_refined_d 0.012 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 4003 Nucleic Acid Atoms Solvent Atoms 952 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing