X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 289.0
Details JCSG+ condition G6, 0.2 M sodium malonate pH 7.0, 20% PEG 3350, Crystal tracking ID 204287g6, 24.5 mg/mL protein concentration, crystallized with the His6-Smt3 fusion tag still on, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 154.6 α = 90
b = 62.19 β = 108.88
c = 85.96 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2009-08-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
2.2 -- 98.8 0.051 -- -- -- -- 39043 -- -3.0 --
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)
2.2 2.26 91.3 0.362 -- 3.48 -- 2657

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 2.2 -- -- 0.0 -- 39042 1950 99.07 -- 0.215 0.213 0.245 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 2.2 2.257 -- 128 2499 0.27 0.323 -- 91.25
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.567
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.03
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.05
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 36.332
r_dihedral_angle_3_deg 12.735
r_chiral_restr 0.085
r_scbond_it 1.79
r_mcbond_it 0.676
r_dihedral_angle_4_deg 16.798
r_scangle_it 2.813
r_bond_refined_d 0.01
r_angle_refined_deg 1.256
r_dihedral_angle_1_deg 5.755
r_gen_planes_refined 0.006
r_mcangle_it 1.264
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3894
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 230

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005