X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5
Temperature 298.0
Details 17% PEG 1000, 0.1 M potassium chloride, 0.1 M sodium acetate, 5 mM DTT, pH 5.0, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.52 α = 63.98
b = 80.85 β = 88.1
c = 89.76 γ = 80.01
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2007-07-11
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.9797 SSRL BL9-2

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 80.58 98.0 0.045 -- -- 4.0 -- 76585 -- -- --

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
MAD 2.0 40.0 -- 0.0 -- 76395 3839 97.78 -- 0.152 0.15 0.202 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 2.052 -- 295 5248 0.138 0.194 -- 96.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.272
Anisotropic B[1][1] -1.07
Anisotropic B[1][2] -0.15
Anisotropic B[1][3] 0.04
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.61
Anisotropic B[3][3] 0.6
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.79
r_gen_planes_other 0.0
r_chiral_restr 0.084
r_mcbond_other 0.341
r_bond_refined_d 0.014
r_dihedral_angle_1_deg 6.89
r_angle_refined_deg 1.092
r_scbond_it 3.153
r_scangle_it 4.866
r_bond_other_d 0.001
r_mcangle_it 1.998
r_dihedral_angle_4_deg 14.804
r_gen_planes_refined 0.004
r_mcbond_it 1.124
r_dihedral_angle_2_deg 39.5
r_dihedral_angle_3_deg 14.755
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9740
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 752

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.2.5
SOLVE phasing version: 2.12
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006