X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.6
Temperature 292.0
Details 5 mg/mL protein, 0.05 M citric acid, 38% v/v PEG200, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 20.5 α = 96.42
b = 27.76 β = 98.6
c = 34.76 γ = 104.46
Symmetry
Space Group P -1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-11-29
Diffraction Radiation
Monochromator Protocol
Cryogenically-cooled single crystal Si(220) side bounce SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.97921 APS 24-ID-E

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
1.6 50 89.3 0.048 -- -- 4.0 9561 8573 -- -3.0 --
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)
1.6 1.64 85.3 0.487 -- 3.5 4.1 384

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 1.6 33.95 -- 0.0 -- 8572 426 89.67 -- 0.2222 0.2208 0.2495 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 1.6 1.642 -- 31 568 0.294 0.388 -- 84.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.4458
Anisotropic B[1][1] -1.25
Anisotropic B[1][2] 0.06
Anisotropic B[1][3] 0.31
Anisotropic B[2][2] 0.57
Anisotropic B[2][3] 0.38
Anisotropic B[3][3] 0.88
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 2.874
r_bond_refined_d 0.023
r_angle_refined_deg 2.036
r_dihedral_angle_1_deg 6.66
r_dihedral_angle_2_deg 40.36
r_dihedral_angle_3_deg 15.429
r_dihedral_angle_4_deg 38.645
r_chiral_restr 0.142
r_gen_planes_refined 0.01
r_mcbond_it 2.626
r_mcangle_it 4.308
r_scbond_it 5.299
r_scangle_it 8.212
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 402
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 14

Software

Computing
Computing Package Purpose
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
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.5.0109 refinement
SCALEPACK data reduction