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Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with AMPPNP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris buffer, 25% Peg3350, 0.1M Na,K tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.615 α = 90 b = 74.563 β = 98.54 c = 89.952 γ = 90
Symmetry Space Group P 1 21 1
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 315 mirrors 2007-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9730 ESRF ID29
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 1.9 50 98.3 0.084 15.1 3 55779 55779
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 1.9 1.97 89.8 0.316 3.5 2.3 5060
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 MOLECULAR REPLACEMENT THROUGHOUT 1.95 10 48474 3799 99.18 0.20563 0.20167 0.203 0.25558 0.2553 RANDOM 21.588
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] 1.03 -1.16 -0.97 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.945 r_dihedral_angle_3_deg 16.448 r_dihedral_angle_4_deg 14.877 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.549 r_scbond_it 2.363 r_angle_refined_deg 1.493 r_mcangle_it 1.47 r_mcbond_it 0.917 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.945 r_dihedral_angle_3_deg 16.448 r_dihedral_angle_4_deg 14.877 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.549 r_scbond_it 2.363 r_angle_refined_deg 1.493 r_mcangle_it 1.47 r_mcbond_it 0.917 r_nbtor_refined 0.301 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5883 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 62
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling