X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 2 microliters of Hmt1 (8mg/ml) in 50 mM Tris, pH 7.0, 50 mM NaCl, 1 mM EDTA, 1 mM DTT + 2 microliters of reservoir:50 mM sodium hepes, pH 7.5, 14% v/v PEG 400, 100 mM CaCl2 + microseeds in 1 microliter of 20 mM sodium citrate, pH 5.6, 15% w/v PEG 4000, 100 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 22K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.1 α = 90
b = 129.43 β = 102.74
c = 101.43 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS monochromator 2000-03-02
Diffraction Radiation
Monochromator Protocol
pair of parallel silicon crystals MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 0.9784,1.0100,0.9500,0.9788 NSLS X12C

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
2.9 28 99.1 0.062 -- -- 3.1 91268 90403 0.0 0.0 56.6
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)
2.89 2.99 95.9 0.235 0.235 5.0 1.8 8739

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
MAD 2.9 28.0 0.0 0.0 45634 46590 4666 99.1 0.253 0.253 0.253 0.294 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 2.9 2.97 816 87 -- 0.333 0.362 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.29
x_bond_d 0.014
x_angle_deg 3.0
x_dihedral_angle_d 25.06
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15520
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
SOLVE phasing
MLPHARE phasing
DM model building
X-PLOR refinement version: 3.851
DENZO data reduction
SCALEPACK data scaling
DM phasing