X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 287.0
Details PEG 8000, ethylene glycol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.98 α = 90
b = 143.16 β = 91.57
c = 71.93 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Osmic Max-Flux confocal focusing mirrors 2002-06-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200HB 1.5418 -- --

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
2.29 24.21 95.8 -- 0.101 -- -- 53761 51511 0.0 0.0 24.0
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)
2.29 2.38 78.3 -- 0.384 1.7 -- 4037

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
FOURIER SYNTHESIS 2.3 24.22 -- 0.0 53547 51411 2608 96.0 -- -- 0.196 0.236 random, same as 1NNM r-free set
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 2.3 2.4 5407 271 -- 0.246 0.286 0.017 80.7
X Ray Diffraction 2.4 2.53 6368 317 -- 0.23 0.287 0.016 95.3
X Ray Diffraction 2.53 2.69 6463 298 -- 0.213 0.282 0.016 96.1
X Ray Diffraction 2.69 2.9 6519 319 -- 0.216 0.286 0.016 97.3
X Ray Diffraction 2.9 3.19 6599 351 -- 0.202 0.248 0.013 98.1
X Ray Diffraction 3.19 3.65 6672 361 -- 0.198 0.226 0.012 99.2
X Ray Diffraction 3.65 4.59 6709 347 -- 0.163 0.198 0.011 99.7
X Ray Diffraction 4.59 24.22 6774 353 -- 0.193 0.215 0.011 99.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.06
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -2.24
Anisotropic B[2][2] -1.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.37
RMS Deviations
Key Refinement Restraint Deviation
c_angle_d 1.18
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.23
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9835
Nucleic Acid Atoms 0
Heterogen Atoms 174
Solvent Atoms 377

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection