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Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 295 2.2 M ammonium sulfate, 50 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 5.60
Crystal Properties Matthews coefficient Solvent content 2.83 56.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.013 α = 90 b = 75.544 β = 90 c = 98.392 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 ADSC QUANTUM 4 2007-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B NSLS X12B
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 1.6 50 97.9 0.048 28.8 6.1 51329
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) 1.6 1.72 99.6 0.39 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1QSP 1.7 17.75 43353 42989 2168 99.2 0.199 0.196 0.23 0.24 0.2573 RANDOM 38.16
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 38.153 r_dihedral_angle_3_deg 17.986 r_dihedral_angle_4_deg 17.835 r_dihedral_angle_1_deg 7.905 r_scangle_it 6.306 r_scbond_it 4.564 r_mcangle_it 3.995 r_mcbond_it 2.793 r_angle_refined_deg 2.565 r_metal_ion_refined 0.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.153 r_dihedral_angle_3_deg 17.986 r_dihedral_angle_4_deg 17.835 r_dihedral_angle_1_deg 7.905 r_scangle_it 6.306 r_scbond_it 4.564 r_mcangle_it 3.995 r_mcbond_it 2.793 r_angle_refined_deg 2.565 r_metal_ion_refined 0.445 r_nbtor_refined 0.311 r_nbd_refined 0.26 r_symmetry_vdw_refined 0.253 r_chiral_restr 0.252 r_xyhbond_nbd_refined 0.203 r_symmetry_hbond_refined 0.142 r_bond_refined_d 0.032 r_gen_planes_refined 0.013 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 2479 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling