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Crystal structure of cerato-platanin 5 from M. perniciosa (MpCP5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M3G PDB ENTRY 3M3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.1 M sodium acetate pH 5.5, 5% PEG 400, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.67 α = 90 b = 107.87 β = 90 c = 112.68 γ = 90
Symmetry Space Group P 21 21 21
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 2011-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.43701 LNLS D03B-MX1
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 1.87 23.02 99.8 0.084 0.084 13.2 6.3 51015 50913 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 1.87 1.97 99.6 0.327 0.327 4.4 6
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 3M3G 1.87 20 48350 48195 2571 99.68 0.16802 0.1651 0.1657 0.2233 0.2252 RANDOM 21.791
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] 2.1 -0.98 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.3 r_dihedral_angle_3_deg 12.277 r_dihedral_angle_4_deg 8.963 r_dihedral_angle_1_deg 6.633 r_scangle_it 4.829 r_scbond_it 3.135 r_mcangle_it 1.891 r_angle_refined_deg 1.887 r_mcbond_it 1.149 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.3 r_dihedral_angle_3_deg 12.277 r_dihedral_angle_4_deg 8.963 r_dihedral_angle_1_deg 6.633 r_scangle_it 4.829 r_scbond_it 3.135 r_mcangle_it 1.891 r_angle_refined_deg 1.887 r_mcbond_it 1.149 r_chiral_restr 0.144 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 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 4180 Nucleic Acid Atoms Solvent Atoms 785 Heterogen Atoms
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling