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Crystal structure of PAM12A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M22 PDB ENTRY 1M22
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 VAPOR DIFFUSION, HANGING DROP, 1.0 M SODIUM ACETATE, 0.1 M HEPES PH 7.0, 0.02M CADMIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.87 α = 90 b = 82.87 β = 90 c = 112.891 γ = 120
Symmetry Space Group P 31 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 110 IMAGE PLATE MAR scanner 345 mm plate HELIOSMX 2014-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H
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 1.8 41.4 100 0.14 12.8 13.2 42172 -3 15.4
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 1.8 1.84 100 0.76 2.1 7.4
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 PDB ENTRY 1M22 1.8 71.77 40001 2108 99.89 0.16159 0.15975 0.19608 0.1903 RANDOM 22.17
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] -0.06 -0.03 -0.06 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.791 r_dihedral_angle_4_deg 17.783 r_dihedral_angle_3_deg 12.808 r_dihedral_angle_1_deg 5.924 r_angle_refined_deg 1.295 r_mcangle_it 1.158 r_scbond_it 1.051 r_angle_other_deg 0.786 r_mcbond_it 0.696 r_mcbond_other 0.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.791 r_dihedral_angle_4_deg 17.783 r_dihedral_angle_3_deg 12.808 r_dihedral_angle_1_deg 5.924 r_angle_refined_deg 1.295 r_mcangle_it 1.158 r_scbond_it 1.051 r_angle_other_deg 0.786 r_mcbond_it 0.696 r_mcbond_other 0.673 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3686 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing