X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 12% to 25% PEG 6000 or PEG 4000 or PEG 3350 or PEG 1450 in the presence of EDTA, DTT and Sodium azide in 100mM MES. pH 6.5, VAPOR DIFFUSION, HANGING DROP at 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.82 α = 90
b = 106.77 β = 90
c = 181.22 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Mirrors 2000-02-10
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
2.8 20 99.5 -- 0.12 -- 3.6 24992 24992 -- -- 38.1
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)
2.8 2.9 98.5 -- 0.314 4.5 3.0 2425

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 2.8 20.0 -- 0.1 24992 23538 2327 93.9 -- -- 0.2316 0.3111 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 2.8 2.9 -- 207 1986 0.427 0.327 -- 89.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Grouped B factor for main chain and side chain atom of individual residues
Mean Isotropic B 14.32
Anisotropic B[1][1] -2.31
Anisotropic B[1][2] 0.55
Anisotropic B[1][3] 1.76
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.8043
c_dihedral_angle_d 22.73
c_angle_deg 1.3458
c_bond_d 0.0079
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.42
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.5
Luzzati Sigma A (R-Free Set) 0.55
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7828
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 150

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 0.4 Structure Refinement
Software
Software Name Purpose
CNS version: 0.4 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection