X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 2-Methyl-2,4-Pentanediol (MPD), Tris-phosphate buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.48 α = 90
b = 50.96 β = 90
c = 118.88 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 124
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Mirrors 2002-03-21
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.54178 -- --

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
1.58 100 94.8 0.049 0.044 -- 14.602 -- 42967 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)
1.58 1.61 87.9 0.394 0.356 2.72 4.24 1824

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 1.58 50.0 0.0 0.0 42697 40622 2038 95.1 -- -- 0.1944 0.219 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 1.58 1.64 3604 184 -- 0.4042 0.409 -- 8.87
X Ray Diffraction 1.64 1.7 3745 216 -- 0.2992 0.3214 -- 9.219
X Ray Diffraction 1.7 1.78 3706 204 -- 0.2417 0.2941 -- 9.123
X Ray Diffraction 1.78 1.87 3759 173 -- 0.2074 0.2414 -- 9.25
X Ray Diffraction 1.87 1.99 3737 191 -- 0.2066 0.2576 -- 9.199
X Ray Diffraction 1.99 2.14 3802 207 -- 0.1983 0.2128 -- 9.35
X Ray Diffraction 2.36 2.7 3962 223 -- 0.1933 0.2192 -- 9.75
X Ray Diffraction 2.7 3.4 4112 214 -- 0.1852 0.1941 -- 10.12
X Ray Diffraction 3.4 50.0 4280 221 -- 0.1622 0.1876 -- 10.53
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.71
RMS Deviations
Key Refinement Restraint Deviation
o_bond_d 0.0048
c_angle_d 2.245
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2384
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 428

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
CNS refinement version: 1.1