X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 290.0
Details Ammonium Sulfate, magnesium chloride, MPD, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.53 α = 90
b = 93.36 β = 90
c = 106.23 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-03-11
IMAGE PLATE RIGAKU RAXIS IV mirrors 2000-03-11
Diffraction Radiation
Monochromator Protocol
Si Crystals SINGLE WAVELENGTH
Ni Filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B 1.000034 NSLS X12B
ROTATING ANODE RIGAKU RU200 -- -- --

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
1.7 35.06 76.0 0.054 -- -- 5.2 92625 73438 -- -3.0 14.2
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)
1.7 1.76 73.9 0.261 -- 1.4 2.1 7040

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 1.7 35.06 -- 2.0 83796 72962 3636 75.9 -- 0.2073 0.206 0.231 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 1.7 1.81 -- 240 4880 0.3332 0.3297 0.021 32.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.3
Anisotropic B[1][1] 6.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.22
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 1.59
c_scbond_it 0.99
c_mcangle_it 1.1
c_mcbond_it 0.65
c_improper_angle_d 0.88
c_bond_d 0.005
c_angle_deg 1.2
c_dihedral_angle_d 22.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.35
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4650
Nucleic Acid Atoms 445
Heterogen Atoms 44
Solvent Atoms 521

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