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Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GBW Poly ala based on the PDB Code 3GBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 2000mM DL Malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.57 52.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.877 α = 90 b = 99.922 β = 90 c = 83.054 γ = 90
Symmetry Space Group C 2 2 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 RAYONIX MX225HE 2009-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9792 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.25 42.8 100 0.13 8.7 7.3 18914 32.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.37 100 0.643 3.7 7.3 2732
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 Poly ala based on the PDB Code 3GBW 2.25 31.94 18890 972 100 0.201 0.198 0.2037 0.256 0.2587 RANDOM 43.016
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.518 r_dihedral_angle_3_deg 15.773 r_dihedral_angle_4_deg 15.641 r_dihedral_angle_1_deg 8.151 r_scangle_it 3.842 r_scbond_it 2.522 r_mcangle_it 1.803 r_angle_refined_deg 1.715 r_mcbond_it 1.17 r_angle_other_deg 0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.518 r_dihedral_angle_3_deg 15.773 r_dihedral_angle_4_deg 15.641 r_dihedral_angle_1_deg 8.151 r_scangle_it 3.842 r_scbond_it 2.522 r_mcangle_it 1.803 r_angle_refined_deg 1.715 r_mcbond_it 1.17 r_angle_other_deg 0.967 r_symmetry_vdw_other 0.265 r_symmetry_vdw_refined 0.253 r_mcbond_other 0.213 r_nbd_refined 0.206 r_nbd_other 0.202 r_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.182 r_chiral_restr 0.105 r_nbtor_other 0.091 r_symmetry_hbond_refined 0.056 r_xyhbond_nbd_other 0.045 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2303 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing