X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 283.0
Details 333mM ammonium sulfate, 10mM magnesium chloride, 50mM sodium chloride, 50mM potassium chloride, 50mM potassium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.58 α = 90
b = 43.08 β = 103.58
c = 56.94 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
CCD ADSC QUANTUM 210 Monochromator 2007-10-07
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9785 ESRF ID14-1

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
2.1 28.69 91.0 0.036 -- -- 2.86 10055 10055 -- 0.0 46.0
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)
2.1 2.18 95.9 0.116 -- 6.4 2.94 1041

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 2.1 10.0 -- 0.0 9497 9497 478 91.26 -- 0.23409 0.23409 0.29491 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 2.1 2.152 693 37 693 0.317 0.374 -- 95.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 26.776
Anisotropic B[1][1] 0.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.53
Anisotropic B[2][2] -1.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.15
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.226
r_scbond_it 2.779
r_symmetry_hbond_refined 0.126
r_symmetry_vdw_refined 0.17
r_metal_ion_refined 0.107
r_xyhbond_nbd_refined 0.219
r_nbtor_refined 0.331
r_nbd_refined 0.342
r_gen_planes_refined 0.016
r_chiral_restr 0.125
r_angle_refined_deg 2.804
r_bond_refined_d 0.019
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.267
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 950
Heterogen Atoms 256
Solvent Atoms 158

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement