X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 294.15
Details 10% MPD(v/v)(Drop), 35% MPD(v/v)(reservoir), 40mM Na-cacodylate trihydrate (pH 7), 12mM spermine tetrahydrochloride, 80mM SrCl2, 20mM MgCl2 hexahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.98 α = 90
b = 43.08 β = 120.98
c = 48.76 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-04-19
Diffraction Radiation
Monochromator Protocol
Si(111) Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.148 SSRL BL7-1

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
1.96 35.81 93.4 0.02 -- -- 2.0 9759 9115 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)
1.96 2.01 96.7 0.31 -- 2.19 1.87 706

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 1.96 35.81 0.0 0.0 9115 8672 443 93.86 0.21839 0.21839 0.21709 0.242 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 1.96 2.011 651 27 651 0.379 0.413 -- 97.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.364
Anisotropic B[1][1] 2.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.93
Anisotropic B[2][2] 1.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.92
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.004
r_gen_planes_refined 0.014
r_chiral_restr 0.082
r_angle_other_deg 1.714
r_angle_refined_deg 1.584
r_bond_other_d 0.009
r_bond_refined_d 0.011
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.171
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 1011
Heterogen Atoms 14
Solvent Atoms 22

Software

Computing
Computing Package Purpose
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
PHASER model building
BLU-ICE data collection