3LDL

Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FZFpdb entry 3FZF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1M Tris buffer, 25% Peg3350, 0.1M Na,K tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.985α = 90
b = 74.326β = 98.81
c = 90.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9730ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35092.50.11102.53039330393
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3887.70.4272.822879

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3FZF2.31528636154892.690.197760.193540.27852RANDOM36
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]
2.39-1.13-1.63-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.46
r_dihedral_angle_3_deg18.466
r_dihedral_angle_4_deg17.667
r_dihedral_angle_1_deg6.668
r_scangle_it2.68
r_scbond_it1.731
r_angle_refined_deg1.532
r_mcangle_it1.228
r_mcbond_it0.711
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.46
r_dihedral_angle_3_deg18.466
r_dihedral_angle_4_deg17.667
r_dihedral_angle_1_deg6.668
r_scangle_it2.68
r_scbond_it1.731
r_angle_refined_deg1.532
r_mcangle_it1.228
r_mcbond_it0.711
r_nbtor_refined0.301
r_nbd_refined0.219
r_symmetry_vdw_refined0.2
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_refined0.183
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5892
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms63

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling