X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 300.0
Details Protein was changed into crystallization buffer (20mM K-HEPES, pH7.5, 10% w/v glycerol, 0.2mM PMSF, 1mM DTT, 4mM Mg-ATP, 0.01% Na-Azide) and concentrated to 18 mg/ml. Crystallization was carried out by setting hanging drops containing 2 ul of protein, (diluted to 13.5mg/ml with 20mM K-Hepes, pH 7.5, 10% glycerol), 0.3 ul 70% glycerol and 1.8 ul of precipitant (20% PEG 4000, 200mM Ammonium sulfate, 100mM Bis-Tris, pH 5.5) over 500ml of the same precipitant solution. Crystals appeared within one day and were of dimensions up to 200 um., VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 144.3 α = 90
b = 144.3 β = 90
c = 159.95 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-04-12
Diffraction Radiation
Monochromator Protocol
Double flat crystal, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.5 ALS 8.3.1

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
2.27 49.27 99.4 -- -- -- 5.6 57296 57296 2.0 2.0 --
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)
2.27 2.35 94.5 -- 62.0 2.0 -- --

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 2.27 49.27 -- 2.0 54226 54226 2867 99.08 -- 0.19954 0.19702 0.24655 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 2.27 2.326 -- 181 3753 0.261 0.335 -- 92.61
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.202
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] -0.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.09
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.618
r_mcangle_it 1.515
r_scangle_it 4.409
r_gen_planes_refined 0.01
r_dihedral_angle_3_deg 20.453
r_bond_refined_d 0.02
r_chiral_restr 0.135
r_angle_refined_deg 1.923
r_scbond_it 2.767
r_dihedral_angle_4_deg 19.884
r_dihedral_angle_2_deg 36.274
r_mcbond_it 0.845
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8420
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 123

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
REFMAC refinement version: 5.4.0067
HKL-2000 data reduction
HKL-2000 data scaling