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Crystal structure of cerato-platanin 2 from M. perniciosa (MpCP2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SUJ PDB entry 3SUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.1 M sodium acetate pH 4.6, 8% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.06 40.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.46 α = 90 b = 85.96 β = 106.82 c = 43.56 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 MAR CCD 165 mm 2010-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45860 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.34 20 92.4 0.065 0.065 22.2 8.3 46732 43181 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.41 87.7 0.27 0.27 8.9 8.2
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 3SUJ 1.34 14.5 44317 41002 2177 92.52 0.17484 0.17322 0.1721 0.20505 0.203 RANDOM 14.173
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] 0.28 0.16 0.26 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.327 r_dihedral_angle_4_deg 18.92 r_dihedral_angle_3_deg 13.091 r_dihedral_angle_1_deg 5.549 r_scangle_it 3.745 r_scbond_it 2.609 r_mcangle_it 1.943 r_angle_refined_deg 1.698 r_mcbond_it 1.314 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.327 r_dihedral_angle_4_deg 18.92 r_dihedral_angle_3_deg 13.091 r_dihedral_angle_1_deg 5.549 r_scangle_it 3.745 r_scbond_it 2.609 r_mcangle_it 1.943 r_angle_refined_deg 1.698 r_mcbond_it 1.314 r_chiral_restr 0.143 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 1782 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms
Software Software Software Name Purpose MAR345 data collection MrBUMP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling