X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6
Details COUNTER-DIFFUSION. protein solution: 250 mM NaCl, 1 mM CaCl2, 10 mM Mes/NaOH, pH 6.0. precipitant solution: 1.4 M (NH4)2SO4, 5% MPD, 50 mM, Mes/NaOH, pH 6.0, 2.4 M Boc-L-Leu

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 157.91 α = 90
b = 157.91 β = 90
c = 104.07 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE mirrors 2010-12-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 SPRING-8 BL41XU

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
1.12 30 100.0 -- -- -- -- 286940 286940 -- -- --

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 1.38 14.0 -- -- -- 146524 7780 99.27 -- 0.13986 0.13922 0.1519 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 1.38 1.415 -- 526 10026 0.253 0.255 -- 98.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.185
Anisotropic B[1][1] 0.04
Anisotropic B[1][2] 0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.05
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 9.251
r_bond_refined_d 0.007
r_bond_other_d 0.0
r_angle_refined_deg 1.194
r_angle_other_deg 0.384
r_dihedral_angle_1_deg 6.169
r_dihedral_angle_2_deg 29.713
r_dihedral_angle_3_deg 10.885
r_dihedral_angle_4_deg 14.022
r_chiral_restr 0.081
r_gen_planes_refined 0.005
r_rigid_bond_restr 0.975
r_sphericity_free 21.819
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2581
Nucleic Acid Atoms 0
Heterogen Atoms 168
Solvent Atoms 419

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
PHASER model building
HKL-2000 data collection