X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.1
Temperature 298.0
Details 21% Polyethylene glycol, 0.150M HEPES-Na, chloride anion traces, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56 α = 90
b = 58.7 β = 90
c = 175.2 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR RIGAKU RAXIS IV -- 2001-11-30
AREA DETECTOR RIGAKU RAXIS IV -- 2001-11-28
IMAGE PLATE RIGAKU RAXIS IV -- 2001-06-27
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
graphite SINGLE WAVELENGTH
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --
ROTATING ANODE RIGAKU 1.5418 -- --
ROTATING ANODE RIGAKU 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
2.1 20 90.0 0.081 -- -- 20.1 32840 31220 -- 0.1 --
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)
2.1 2.17 56.9 0.306 -- 1.4 1.54 1935

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 2.1 8.0 -- 2.0 30567 28245 1423 83.36 -- -- 0.231 0.269 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 2.1 2.19 1752 91 -- 0.3754 0.3774 -- 42.03
X Ray Diffraction 2.19 2.31 2799 145 -- 0.3622 0.371 -- 67.24
X Ray Diffraction 2.31 2.45 3343 153 -- 0.337 0.3749 -- 79.27
X Ray Diffraction 2.45 2.63 3572 184 -- 0.3375 0.3346 -- 85.7
X Ray Diffraction 2.63 2.88 3957 206 -- 0.3294 0.3558 -- 93.77
X Ray Diffraction 2.88 3.28 4165 201 -- 0.2763 0.3326 -- 97.88
X Ray Diffraction 3.28 4.04 4251 214 -- 0.1941 0.2484 -- 99.39
X Ray Diffraction 4.04 8.0 4406 229 -- 0.16 0.2001 -- 99.77
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 51.72
Anisotropic B[1][1] -1.093
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.437
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.531
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 7.0
x_scbond_it 3.0
x_mcangle_it 5.0
x_mcbond_it 2.5
x_improper_angle_d 1.858
x_dihedral_angle_d 22.06
x_angle_deg 1.764
x_bond_d 0.013
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.44
Luzzati Sigma A (Observed) 0.54
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.47
Luzzati Sigma A (R-Free Set) 0.43
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4384
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 437

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR model building
SCALEPACK data reduction
DENZO data collection