X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details 25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.26 α = 90
b = 108.73 β = 90
c = 136.5 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-07-02
Diffraction Radiation
Monochromator Protocol
Silicon (1 1 1) channel-cut SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.9465 ESRF ID23-1

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
1.4 30 91.5 -- 0.072 -- 4.0 309048 282740 0.0 0.0 21.0
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)
1.4 1.48 60.5 -- 0.994 0.87 2.9 28469

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 1.4 25.0 0.0 0.0 309018 268420 14302 91.49 -- 0.12906 0.12698 0.16804 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 1.4 1.436 12445 669 11866 0.32 0.342 -- 55.24
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic temperature factors
Mean Isotropic B 18.912
Anisotropic B[1][1] -0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.93
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.012
r_dihedral_angle_1_deg 5.578
r_dihedral_angle_2_deg 36.284
r_mcbond_it 2.333
r_angle_refined_deg 1.317
r_dihedral_angle_3_deg 11.504
r_scbond_it 4.7
r_chiral_restr 0.092
r_mcangle_it 3.351
r_rigid_bond_restr 2.471
r_dihedral_angle_4_deg 17.571
r_gen_planes_refined 0.007
r_scangle_it 6.503
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.059
Luzzati ESD (R-Free Set) 0.057
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11915
Nucleic Acid Atoms 0
Heterogen Atoms 98
Solvent Atoms 1775

Software

Software
Software Name Purpose
MxCuBE data collection
PHASER phasing
REFMAC refinement version: 5.5.0109
XDS data reduction
XSCALE data scaling