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Crystal structure of Pichia pastoris Lysyl Oxidase PPLO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAC PDB ENTRY 1OAC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 25% PEG 4000, 0.175M ammonium sulfate, 15% MPD, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 248.442 α = 90 b = 121.125 β = 124.64 c = 151.841 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE MAR scanner 345 mm plate 2001-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
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 1.65 24.6 94.7 0.062 9.1 2.8 419014
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 1.65 1.69 0.42 2.2 2.6
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 (All) 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, EXCEPT FINAL ROUND PDB ENTRY 1OAC 1.65 24.6 419014 20998 94.7 0.16029 0.16029 0.1605 0.1657 0.18673 0.1727 RANDOM 17.86
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] 0.5 0.58 0.21 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.4 r_scangle_it 5.983 r_dihedral_angle_1_deg 5.589 r_scbond_it 3.852 r_mcangle_it 2.52 r_mcbond_it 1.604 r_angle_refined_deg 1.517 r_nbd_refined 0.346 r_symmetry_hbond_refined 0.199 r_symmetry_vdw_refined 0.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.4 r_scangle_it 5.983 r_dihedral_angle_1_deg 5.589 r_scbond_it 3.852 r_mcangle_it 2.52 r_mcbond_it 1.604 r_angle_refined_deg 1.517 r_nbd_refined 0.346 r_symmetry_hbond_refined 0.199 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.108 r_bond_refined_d 0.01 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 23704 Nucleic Acid Atoms Solvent Atoms 3981 Heterogen Atoms 488
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling