X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 294.0
Details 0.5-1.5M sodium malonate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 154.97 α = 90
b = 39.03 β = 131.81
c = 107.62 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 MARMOSAIC 225 mm CCD -- 2008-02-13
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-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
2.55 80.32 93.6 -- 0.381 -- 3.4 15222 15222 -- -- --
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)
2.55 2.64 58.5 -- 0.382 2.2 1.9 --

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 2.55 80.32 -- -- 14423 14423 761 94.42 -- 0.22458 0.22128 0.28777 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 2.55 2.616 -- 32 665 0.272 0.308 -- 59.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.274
Anisotropic B[1][1] -0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.97
Anisotropic B[2][2] -0.3
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.8
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 19.47
r_scbond_it 1.329
r_mcbond_it 0.548
r_bond_refined_d 0.009
r_chiral_restr 0.082
r_gen_planes_refined 0.004
r_scangle_it 2.222
r_dihedral_angle_3_deg 16.457
r_mcangle_it 1.059
r_dihedral_angle_2_deg 32.866
r_dihedral_angle_1_deg 7.147
r_angle_refined_deg 1.231
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2615
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 34

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
REFMAC refinement version: 5.5.0072
HKL-2000 data reduction
HKL-2000 data scaling