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
c_angle_d 2.245
o_bond_d 0.0048
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 2376
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 428

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection