X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 293.0
Details 0.1 M NA ACETATE PH 4.5, 25% PEG 3350, 0.2 M LITHIUM SULFATE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.14 α = 90
b = 88.14 β = 90
c = 219.59 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 VARIMAX HF 2013-12-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
2.3 30 93.8 0.057 -- -- 15.4 -- 21683 -- -3.0 37.3
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)
2.3 2.37 68.4 0.324 -- 5.5 7.1 --

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
FOURIER SYNTHESIS 2.3 10.0 -- 0.0 -- 20255 1089 92.4 -- 0.30196 0.29775 0.3828 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 2.306 2.363 -- 47 996 0.348 0.599 -- 67.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.3
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 6.439
r_bond_refined_d 0.005
r_dihedral_angle_4_deg 19.798
r_dihedral_angle_3_deg 16.077
r_scbond_it 4.218
r_angle_refined_deg 1.039
r_dihedral_angle_1_deg 5.759
r_gen_planes_refined 0.004
r_chiral_restr 0.065
r_mcbond_it 4.187
r_long_range_B_refined 10.46
r_dihedral_angle_2_deg 32.686
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3196
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 70

Software

Software
Software Name Purpose
XDS data reduction
XDS data scaling
REFMAC phasing
REFMAC refinement version: 5.8.0049