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Crystal structure of hemopexin fold protein CP4 from cow pea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 50mM Tris-HCl, 30% PEG 8000 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.087 α = 90 b = 60.138 β = 111.18 c = 67.574 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 120 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2004-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.1 100 97.4 0.105 27508
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 2.1 2.154 95.4 0.322 1.13 5.1 490
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3LP9 2.1 26.22 22725 2517 91.84 0.20895 0.20481 0.2023 0.24648 0.2427 RANDOM 16.171
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] -0.35 -0.66 -0.64 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.525 r_dihedral_angle_4_deg 18.565 r_dihedral_angle_3_deg 14.556 r_dihedral_angle_1_deg 4.529 r_mcangle_it 3.678 r_scangle_it 2.992 r_mcbond_it 2.51 r_scbond_it 1.979 r_angle_refined_deg 1.647 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.525 r_dihedral_angle_4_deg 18.565 r_dihedral_angle_3_deg 14.556 r_dihedral_angle_1_deg 4.529 r_mcangle_it 3.678 r_scangle_it 2.992 r_mcbond_it 2.51 r_scbond_it 1.979 r_angle_refined_deg 1.647 r_nbtor_refined 0.322 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3504 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 6
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction