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Crystal Structure of Protein from Mouse Mm.236127
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 PROTEIN SOLUTION (10 MG/ML REDUCTIVELY METHYLATED PROTEIN,
0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE,
0.0003 M TCEP, 0.005 BisTris PH 7.0) MIXED IN A 1:1 RATIO WITH THE
WELL SOLUTION (0.3 M NaH2PO4, 1.7 M K2HPO4) AND CRYOPROTECTED WITH FOMBLIN FOLLOWED BY PARATONE N, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.586 α = 90 b = 68.078 β = 90 c = 190.982 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 MARMOSAIC 300 mm CCD ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY 2006-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 2.2 46.5 96.1 0.079 13.469 12.9 30718
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) 2.2 2.28 73.4 0.35 3.344 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.2 46.5 30651 1546 96 0.227 0.224 0.2478 0.282 0.2925 RANDOM 25.85
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] 1.786 0.354 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.179 r_dihedral_angle_3_deg 17.586 r_dihedral_angle_4_deg 16.782 r_dihedral_angle_1_deg 6.758 r_scangle_it 3.323 r_scbond_it 2.291 r_angle_refined_deg 1.688 r_mcangle_it 1.32 r_mcbond_it 0.861 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.179 r_dihedral_angle_3_deg 17.586 r_dihedral_angle_4_deg 16.782 r_dihedral_angle_1_deg 6.758 r_scangle_it 3.323 r_scbond_it 2.291 r_angle_refined_deg 1.688 r_mcangle_it 1.32 r_mcbond_it 0.861 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.27 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.168 r_chiral_restr 0.111 r_metal_ion_refined 0.105 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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_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 3938 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 32
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction ARP/wARP model building