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Crystal structure of an enzyme from Penicillium herquei in condition2
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 PEG4000, 0.1 M Imidazole pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.73 54.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.617 α = 90 b = 74.617 β = 90 c = 108.926 γ = 120
Symmetry Space Group P 62 2 2
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 1.62 25 99.2 0.048 0.05 0.011 19.7 20 23321
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 1.62 1.68 100 0.463 0.474 0.103 0.991 20.8
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 1.62 24.44 22115 1116 98.99 0.18627 0.18543 0.20229 0.2595 RANDOM 34.539
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] 1.15 0.57 1.15 -3.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.56 r_dihedral_angle_3_deg 12.175 r_dihedral_angle_4_deg 10.926 r_dihedral_angle_1_deg 8.26 r_long_range_B_refined 7.271 r_long_range_B_other 7.194 r_scangle_other 6.535 r_scbond_other 4.802 r_scbond_it 4.801 r_mcangle_other 3.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.56 r_dihedral_angle_3_deg 12.175 r_dihedral_angle_4_deg 10.926 r_dihedral_angle_1_deg 8.26 r_long_range_B_refined 7.271 r_long_range_B_other 7.194 r_scangle_other 6.535 r_scbond_other 4.802 r_scbond_it 4.801 r_mcangle_other 3.811 r_mcangle_it 3.788 r_mcbond_it 2.859 r_mcbond_other 2.561 r_angle_refined_deg 1.499 r_angle_other_deg 1.458 r_chiral_restr 0.112 r_gen_planes_refined 0.013 r_bond_refined_d 0.01 r_gen_planes_other 0.002 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 997 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing