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Structure of mif with HPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GAD PDB ENTRY 3GAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 4.6 289 2.5M Ammonium sulfate, 0.1M Sodium acetate trihydrate pH4.6, hanging drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.26 62.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.5 α = 90 b = 99.53 β = 90 c = 106.6 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 2008-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.0 BSRF 3W1A
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 72.74 99.8 0.064 59842 -3 26.963
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) 2.1 2.2 98.6 0.235 7.9
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 PDB ENTRY 3GAD 2.1 47.75 58009 1832 99.81 0.1588 0.15774 0.1676 0.19108 0.1987 RANDOM 21.275
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.431 r_dihedral_angle_4_deg 16.335 r_dihedral_angle_3_deg 13.087 r_dihedral_angle_1_deg 4.551 r_scangle_it 2.313 r_scbond_it 1.493 r_mcangle_it 1.03 r_angle_refined_deg 0.956 r_mcbond_it 0.604 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.431 r_dihedral_angle_4_deg 16.335 r_dihedral_angle_3_deg 13.087 r_dihedral_angle_1_deg 4.551 r_scangle_it 2.313 r_scbond_it 1.493 r_mcangle_it 1.03 r_angle_refined_deg 0.956 r_mcbond_it 0.604 r_nbtor_refined 0.299 r_symmetry_hbond_refined 0.2 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 5618 Nucleic Acid Atoms Solvent Atoms 788 Heterogen Atoms 55
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction