X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 291.0
Details sodium citrate 100mM, lithium sulfate 1.2 M, ammonium sulfate 0.5 M, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.56 α = 90
b = 111.56 β = 90
c = 56.33 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirror 2000-09-10
CCD MARRESEARCH mirror 2000-09-09
Diffraction Radiation
Monochromator Protocol
Si [111] channel MAD
diamond [111] crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.83211, 1.00474, 1.00850 ESRF BM14
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
2.4 27.96 99.8 0.062 0.051 -- 5.5 16248 16035 1.0 0.0 50.8
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)
2.4 2.53 99.6 0.432 0.358 1.7 5.2 2178

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 2.4 27.96 -- 1.0 16049 16035 945 99.9 0.275 0.275 0.231 0.257 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 2.4 2.51 1960 100 1860 0.307 0.307 0.031 99.9
X Ray Diffraction 2.51 2.64 1978 113 1865 0.306 0.307 0.029 99.6
X Ray Diffraction 2.64 2.81 1997 117 1880 0.282 0.283 0.026 99.9
X Ray Diffraction 2.81 3.02 1978 113 1865 0.251 0.251 0.024 99.7
X Ray Diffraction 3.02 3.33 2001 120 1881 0.252 0.252 0.023 99.8
X Ray Diffraction 3.33 3.81 2003 119 1884 0.217 0.217 0.02 100.0
X Ray Diffraction 3.81 4.79 2026 130 1896 0.194 0.193 0.017 100.0
X Ray Diffraction 4.79 27.96 2092 133 1959 0.22 0.221 0.019 99.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.2
Anisotropic B[1][1] 5.92
Anisotropic B[1][2] 4.39
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.84
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 1.4
x_torsion_impr_deg 0.97
x_bond_d 0.01
x_torsion_deg 23.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.37
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.35
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2042
Nucleic Acid Atoms 0
Heterogen Atoms 51
Solvent Atoms 65

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
CCP4 data scaling version: (SCALA)
MLPHARE phasing