X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 0.2 M AMMONIUM ACETATE, 0.15 M MAGNESIUM ACETATE, 5% W/V PEG 4000, 50 MM HEPES BUFFER, PH 7.0 AT 24 DEGREES C

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.09 α = 90
b = 104.07 β = 90
c = 116.18 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 RAXIS4 MIRRORS 2000-06-10
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
2.65 20 94.5 -- 0.047 -- 3.436 -- 17550 -- 0.0 40.9
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)
2.65 2.7 88.9 -- 0.092 10.9 2.91 --

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 2.65 18.01 -- 0.0 -- 17550 876 94.5 -- 0.223 0.223 0.263 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 2.65 2.82 -- 127 2561 0.416 0.409 0.036 88.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 52.4
Anisotropic B[1][1] -25.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -21.77
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 47.69
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 5.89
c_scangle_it 8.14
c_mcbond_it 4.43
c_mcangle_it 6.55
c_bond_d 0.008
c_dihedral_angle_d 23.6
c_improper_angle_d 1.13
c_angle_deg 1.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.38
Luzzati Sigma A (Observed) 0.58
Luzzati Resolution Cutoff (Low) 20.0
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.7
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1826
Nucleic Acid Atoms 1300
Heterogen Atoms 0
Solvent Atoms 58

Software

Software
Software Name Purpose
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling
CNS phasing version: 0.9