X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details Precipitant: 25 % wt/vol PEG 2000, 200mM MgCl2, 100 mM sodium cacodylate, pH 6.5 Sample: Hsp90a-NTD 20 mg/mL, 10 mM AMPCPP, 500 mM NaCl, 20 mM TRIS, pH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.08 α = 90
b = 44.12 β = 116.41
c = 54.51 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2018-04-29
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
2.05 48.82 99.9 0.072 -- -- 3.2 -- 14639 -- 2.0 18.5
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.05 2.16 99.9 0.363 -- 2.8 3.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.05 48.48 -- -- -- 13930 700 99.84 -- 0.17237 0.16943 0.23196 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.05 2.103 -- 51 1020 0.207 0.301 -- 99.72
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.331
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.05
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.09
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.012
r_chiral_restr 0.166
r_dihedral_angle_4_deg 16.453
r_mcbond_it 1.831
r_mcangle_it 2.762
r_gen_planes_refined 0.011
r_scbond_it 2.441
r_angle_refined_deg 2.111
r_dihedral_angle_2_deg 34.497
r_dihedral_angle_1_deg 7.53
r_dihedral_angle_3_deg 16.606
r_long_range_B_refined 5.671
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1733
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 192

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0222
XDS data reduction
SCALA data scaling
MOLREP phasing