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MBP-MamC loop structure, a magnetite biomineralizing protein from Magnetospirillium magneticum AMB-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium acetate ,
2 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.6 α = 90 b = 66.6 β = 90 c = 211.137 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 315r 2013-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
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 2.8 63.52 95.23 0.147 24.64 7.2 11938
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 3PUZ 2.8 63.52 11241 596 95.27 0.26958 0.26747 0.30725 0.2751 RANDOM 50.074
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] 4.27 4.27 -8.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.038 r_dihedral_angle_3_deg 13.573 r_dihedral_angle_4_deg 10.901 r_dihedral_angle_1_deg 4.586 r_long_range_B_refined 1.565 r_long_range_B_other 1.565 r_angle_refined_deg 0.837 r_angle_other_deg 0.686 r_mcangle_it 0.326 r_mcangle_other 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.038 r_dihedral_angle_3_deg 13.573 r_dihedral_angle_4_deg 10.901 r_dihedral_angle_1_deg 4.586 r_long_range_B_refined 1.565 r_long_range_B_other 1.565 r_angle_refined_deg 0.837 r_angle_other_deg 0.686 r_mcangle_it 0.326 r_mcangle_other 0.326 r_scangle_other 0.197 r_mcbond_it 0.174 r_mcbond_other 0.174 r_scbond_it 0.103 r_scbond_other 0.103 r_chiral_restr 0.048 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2952 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing