X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 0.1 M KCL, 0.05 MGSO4, 4% V/V MPD, 6% V/V GLYCEROL, 0.05 M NA HEPES PH 7.0 AT 24 DEGREES C

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.68 α = 90
b = 73.38 β = 90
c = 161.7 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 RIGAKU RAXIS IV MIRRORS 1998-11-17
Diffraction Radiation
Monochromator Protocol
DIAMOND SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45XU -- SPRING-8 BL45XU

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
2.45 20 99.0 -- 0.072 -- 7.496 -- 27451 -- 0.0 67.0
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)
2.45 2.54 95.5 -- 0.397 2.162 4.0 --

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 2.45 19.94 -- 0.0 -- 27319 1339 98.1 -- 0.229 0.229 0.267 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 2.45 2.6 -- 213 3725 0.422 0.393 0.027 85.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 65.6
Anisotropic B[1][1] 12.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -18.7
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 14.78
c_scbond_it 12.38
c_mcangle_it 9.81
c_mcbond_it 6.93
c_improper_angle_d 1.14
c_bond_d 0.005
c_angle_deg 1.1
c_dihedral_angle_d 18.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.38
Luzzati Sigma A (Observed) 0.6
Luzzati Resolution Cutoff (Low) 20.0
Luzzati ESD (R-Free Set) 0.45
Luzzati Sigma A (R-Free Set) 0.71
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2080
Nucleic Acid Atoms 1060
Heterogen Atoms 2
Solvent Atoms 123

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.851 Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
CNS version: 0.9 refinement
X-PLOR version: 3.851 model building