X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details Protein buffer: 50 mM HEPES, pH 7.5, 5 mM TCEP. Protein was incubated on ice with 5 mM ligand (1:20 dilution of 100 mM stock in H2O for AMPPNP or DMSO for PHA-680626) for 0.5-1 h, followed by a brief centrifugation step and drop setting at RT (0.5 microliter protein + 0.5 microliter reservoir solution consisting of 500 mM magnesium acetate, 10 % PEG 4000 and 0.3 mM zinc acetate for AMPPNP, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.96 α = 90
b = 65.96 β = 90
c = 154.04 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2006-02-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID -- APS 17-ID

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
2.4 45.9 -- -- 0.063 -- 5.6 -- 14898 -- -- --
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)
2.4 2.49 71.6 -- 0.319 1.85 3.9 817

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 2.4 45.9 -- -- -- 14116 757 93.98 -- 0.20463 0.20302 0.23534 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 2.4 2.463 -- 49 751 0.297 0.35 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.44
Anisotropic B[1][1] 4.25
Anisotropic B[1][2] 2.12
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.37
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.164
r_angle_refined_deg 1.246
r_chiral_restr 0.149
r_gen_planes_refined 0.004
r_symmetry_vdw_other 0.212
r_dihedral_angle_1_deg 6.08
r_nbd_refined 0.181
r_bond_refined_d 0.009
r_symmetry_vdw_refined 0.171
r_angle_other_deg 0.887
r_scbond_it 1.051
r_bond_other_d 0.002
r_mcbond_it 0.421
r_mcangle_it 0.796
r_scangle_it 1.823
r_gen_planes_other 0.004
r_symmetry_hbond_refined 0.374
r_metal_ion_refined 0.042
r_nbd_other 0.217
r_nbtor_other 0.082
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2366
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 97

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
JDirector data collection
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing