X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.1
Temperature 292.0
Details 2.2 M ammonium sulfate, 0.1 M citric acid pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.4 α = 90
b = 162.13 β = 90
c = 45.28 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2011-07-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.99188 ESRF ID29

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
1.55 24.6 99.4 -- -- -- -- -- 83099 -- -- --
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)
1.55 1.63 98.5 -- -- -- -- --

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
PDB ENTRY 3DPO 1.55 24.6 -- -- -- 80303 1624 97.92 -- 0.21284 0.21228 0.24053 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 1.55 1.59 -- 109 5870 0.294 0.379 -- 98.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.424
Anisotropic B[1][1] -1.6
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.36
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 15.517
r_dihedral_angle_2_deg 39.052
r_dihedral_angle_4_deg 17.253
r_angle_refined_deg 2.34
r_dihedral_angle_1_deg 5.453
r_gen_planes_refined 0.013
r_bond_refined_d 0.022
r_chiral_restr 0.199
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3400
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 386

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0029
XDS data reduction
SCALA data scaling