X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details protein solution: 15 mg/ml protein, 20 mM Tris pH 8.0, 200 mM NaCl, 10 % glycerol well solution: 200 mM MgCl2, 100 mM Bis-Tris pH 6.5, 25% PEG3350 protein and well solutions mixed 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.45 α = 84.2
b = 98.41 β = 89.8
c = 100.88 γ = 83.8
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirrors 2009-06-20
Diffraction Radiation
Monochromator Protocol
Si 111 Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.9724 APS 23-ID-D

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
2.5 30 98.4 0.109 0.109 -- 3.9 76049 74832 -3.0 -3.0 51.2

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 2.52 30.0 -- -- 73265 73265 1489 100.0 0.20709 0.20709 0.20581 0.26871 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 2.516 2.581 -- 90 4746 0.265 0.372 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic, + TLS
Mean Isotropic B 47.597
Anisotropic B[1][1] 2.0
Anisotropic B[1][2] -0.12
Anisotropic B[1][3] 0.87
Anisotropic B[2][2] 1.21
Anisotropic B[2][3] -0.67
Anisotropic B[3][3] -3.06
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 9.264
r_scbond_it 6.855
r_mcangle_it 4.673
r_mcbond_it 2.732
r_gen_planes_refined 0.011
r_chiral_restr 0.148
r_dihedral_angle_4_deg 19.963
r_dihedral_angle_3_deg 22.804
r_dihedral_angle_2_deg 36.576
r_dihedral_angle_1_deg 7.974
r_angle_refined_deg 2.151
r_bond_refined_d 0.023
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12557
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
BluIce Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
MOLREP model building
BluIce data collection