X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 291.0
Details 100 mM NaOAc, 0.75 M KF, 2.2 M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.12 α = 90
b = 100.12 β = 90
c = 293.3 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2009-04-24
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2

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
3.8 70.2 96.1 -- 0.103 -- -- 15622 14852 0.0 0.0 --
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)
3.8 4.01 97.9 -- 0.608 1.3 3.0 --

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 3.8 70.01 0.0 0.0 0 14727 711 94.28 0.293 0.293 0.291 0.329 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 3.8 3.885 -- 47 969 0.384 0.497 -- 93.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 88.009
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 17.281
MAIN-CHAIN BOND REFINED ATOMS (A''2) 0.494
SIDE-CHAIN BOND REFINED ATOMS (A''2) 0.894
r_angle_refined_deg 1.352
r_dihedral_angle_4_deg 12.058
SIDE-CHAIN ANGLE REFINED ATOMS (A''2) 1.576
r_dihedral_angle_1_deg 5.666
r_gen_planes_refined 0.004
CHIRAL-CENTER RESTRAINTS (A''3) 0.058
r_bond_refined_d 0.007
r_dihedral_angle_2_deg 34.193
MAIN-CHAIN ANGLE REFINED ATOMS (A''2) 0.924
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1725
Nucleic Acid Atoms 4659
Heterogen Atoms 6
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0066
PDB_EXTRACT data extraction version: 3.005
MxCuBE data collection
MOSFLM data reduction
SCALA data scaling
PHASER phasing