X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details PROTEIN/DNA COMPLEX CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION METHOD AT 27 DEGREES CELSIUS. THE RESEVOIR CONTAINS 50 MM MORPHOLINO-SULFONIC ACID PH7.0, 250MM AMMONIUM CHLORIDE, 30 % PEG 4000, 5 MM DTT. THE DROPS CONTAINED A 1:1 RATIO OF PROTEIN-COMPLEX TO RESEVOIR.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.42 α = 90
b = 34.24 β = 109.13
c = 56.26 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRROR --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B -- NSLS X12B

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
2.7 18 95.0 -- 0.073 -- 2.3 -- 5200 -- 3.0 80.3
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)
2.7 2.8 96.9 -- 0.368 3.1 -- --

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 2.7 18.0 -- 0.0 -- 5200 568 95.0 -- -- 0.219 0.295 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 2.7 2.87 -- 97 787 0.35 0.42 0.04 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.8
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
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_mcangle_it 4.83
c_angle_deg 2.4
c_improper_angle_d 1.78
c_scbond_it 4.36
c_mcbond_it 3.06
c_dihedral_angle_d 21.6
c_bond_d 0.016
c_scangle_it 6.34
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.51
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.45
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 690
Nucleic Acid Atoms 650
Heterogen Atoms 2
Solvent Atoms 38

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR, MLPHARE Structure Solution
CNS 0.5 Structure Refinement
Software
Software Name Purpose
MLPHARE model building
CNS version: 0.5 refinement
X-PLOR model building
DENZO data collection
SCALEPACK data reduction