X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.8
Temperature 277.0
Details 100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8, vapor diffusion, temperature 277K, VAPOR DIFFUSION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.38 α = 90
b = 41.43 β = 104.66
c = 72.5 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
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.100 NSLS X25

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
1.5 50 91.7 0.044 -- -- 4.9 -- 36000 -- -- --
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)
1.5 1.53 51.7 0.191 -- -- 2.7 1024

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 1.5 35.67 -- 0.0 -- 35941 1816 91.56 -- 0.1528 0.1509 0.1908 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 1.5 1.539 -- 82 1464 0.182 0.234 -- 53.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.6519
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
r_bond_refined_d 0.028
r_dihedral_angle_1_deg 6.835
r_angle_refined_deg 2.402
r_dihedral_angle_4_deg 22.554
r_dihedral_angle_2_deg 36.524
r_mcangle_it 2.476
r_chiral_restr 0.193
r_dihedral_angle_3_deg 13.145
r_mcbond_it 1.514
r_scbond_it 3.37
r_gen_planes_refined 0.015
r_scangle_it 5.179
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2039
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 304

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10