X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Microbatch Under Oil
pH 7.33
Temperature 298.0
Details 1 mg/ml protein, 16.5% PEG 3350 (final concentration in drop v/v), 0.1 M Hepes, pH 7.33, microbatch under oil, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.21 α = 89.91
b = 54.98 β = 86.44
c = 93.47 γ = 78.63
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification) 2011-05-29
Diffraction Radiation
Monochromator Protocol
BARTELS MONOCROMATOR SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
Synchrotron SLS BEAMLINE X06DA 0.9792 SLS X06DA

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
2.5 50 97.5 0.116 -- -- -- 52900 25885 0.0 0.0 --
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)
2.5 2.6 97.7 0.48 -- 4.05 -- --

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
SAD 2.5 46.89 -- -- 52900 24589 1295 97.87 -- 0.2118 0.20921 0.26109 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 2.5 2.565 -- 96 1816 0.265 0.35 -- 97.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.803
Anisotropic B[1][1] 2.04
Anisotropic B[1][2] -0.92
Anisotropic B[1][3] 0.8
Anisotropic B[2][2] -0.52
Anisotropic B[2][3] -0.04
Anisotropic B[3][3] -1.26
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.007
r_chiral_restr 0.12
r_dihedral_angle_4_deg 15.12
r_dihedral_angle_3_deg 19.855
r_dihedral_angle_2_deg 38.369
r_dihedral_angle_1_deg 7.139
r_angle_refined_deg 1.762
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5412
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 399

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
RESOLVE version: 2.15 density modification
SOLVE version: 2.13 phasing
Xscale data reduction