X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 278.0
Details 100 mM MOPS (pH 7.0), 250 mM MgCl2, 11% PEG 8000, 1 mM TCEP, 2 mM Thymol, 1 mM MgCl2, 2 mM ADP, and 3 mM sodium vanadate, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.11 α = 90
b = 145.77 β = 90
c = 152.91 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2004-08-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 32-ID 0.708 APS 32-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 40 99.8 0.062 -- -- 5.8 -- 63478 0.0 0.0 33.4
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)
2.0 2.07 98.2 0.269 -- 3.7 5.1 63478

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 2.0 40.0 -- 0.0 -- 63478 3388 99.51 0.17514 0.17514 0.17298 0.21498 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 2.0 2.046 -- 221 4463 0.256 0.298 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.417
Anisotropic B[1][1] 0.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.8
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.756
r_scbond_it 3.059
r_mcangle_it 2.072
r_mcbond_it 1.174
r_symmetry_hbond_refined 0.205
r_symmetry_vdw_other 0.326
r_symmetry_vdw_refined 0.126
r_metal_ion_refined 0.25
r_bond_refined_d 0.022
r_bond_other_d 0.002
r_angle_refined_deg 1.685
r_angle_other_deg 1.07
r_dihedral_angle_1_deg 5.928
r_chiral_restr 0.116
r_gen_planes_refined 0.011
r_gen_planes_other 0.013
r_nbd_refined 0.226
r_nbd_other 0.248
r_nbtor_other 0.089
r_xyhbond_nbd_refined 0.185
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5461
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 678

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement