X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.8
Temperature 291.0
Details Reservoir solution: 16 % PEG 4000, 0.2M potassium phosphate, 10 % glycerol. Protein solution: 16 mM sodium phosphate, 0.1 M NaCl, 10 % glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.35 α = 90
b = 92.35 β = 90
c = 143.46 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2009-05-06
Diffraction Radiation
Monochromator Protocol
SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-3 0.97926 MAX II I911-3

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 48.28 99.9 0.092 -- -- 7.2 22173 22173 2.0 2.0 --
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 2.64 100.0 0.346 -- 4.3 7.3 3160

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 46.17 -- -- 20985 20985 1130 99.78 0.22753 0.22753 0.22491 0.2755 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 1524 84 1524 0.323 0.38 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.468
Anisotropic B[1][1] -0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.21
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 4.666
r_dihedral_angle_3_deg 16.997
r_dihedral_angle_2_deg 36.361
r_bond_refined_d 0.015
r_chiral_restr 0.1
r_scbond_it 2.434
r_scangle_it 3.871
r_angle_refined_deg 1.336
r_gen_planes_refined 0.008
r_dihedral_angle_4_deg 17.008
r_mcbond_it 0.708
r_mcangle_it 1.334
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3904
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 43

Software

Software
Software Name Purpose
MAR345 data collection
PHENIX model building
REFMAC refinement version: 5.5.0072
MOSFLM data reduction
SCALA data scaling
PHENIX phasing