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Crystal structure of Synbindin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 2% MPD, 3% EG, 1% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.15 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.391 α = 90 b = 124.391 β = 90 c = 124.391 γ = 90
Symmetry Space Group P 21 3
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 2005-02-19 M MAD 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2006-04-11 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 0.9787, 0.9500, 0.9793 BSRF 3W1A 2 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
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 2.8 50 99.8 0.044 16132 2 2 91.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.8 30.17 14891 792 97.49 0.24512 0.2427 0.28962 0.2802 RANDOM 73.717
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.483 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_4_deg 15.977 r_dihedral_angle_1_deg 4.953 r_scangle_it 3.105 r_mcangle_it 2.322 r_scbond_it 2.255 r_mcbond_it 1.604 r_angle_refined_deg 1.067 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.483 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_4_deg 15.977 r_dihedral_angle_1_deg 4.953 r_scangle_it 3.105 r_mcangle_it 2.322 r_scbond_it 2.255 r_mcbond_it 1.604 r_angle_refined_deg 1.067 r_nbtor_refined 0.305 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.07 r_bond_refined_d 0.008 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 3205 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection