X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 277.0
Details NANODROP, 0.2M NH4OAc, 30.0% PEG 4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.78 α = 90
b = 125.27 β = 90
c = 174.65 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-02-21
Diffraction Radiation
Monochromator Protocol
Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97911, 0.97922 SSRL BL9-2

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
1.7 28.04 98.5 0.056 -- -- -- -- 60062 -- -3.0 15.794
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)
1.7 1.76 97.1 0.328 -- 2.5 -- --

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
MAD 1.7 28.039 -- 0.0 -- 60025 3037 99.2 -- 0.142 0.14 0.166 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 1.7 1.744 -- 228 4096 0.189 0.212 -- 97.61
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.202
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.49
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.003
r_dihedral_angle_1_deg 6.169
r_scbond_it 2.237
r_scangle_it 3.597
r_angle_other_deg 1.413
r_mcbond_it 0.774
r_chiral_restr 0.1
r_dihedral_angle_4_deg 18.925
r_dihedral_angle_2_deg 40.212
r_mcbond_other 0.268
r_bond_other_d 0.001
r_mcangle_it 1.289
r_bond_refined_d 0.016
r_gen_planes_refined 0.009
r_angle_refined_deg 1.521
r_dihedral_angle_3_deg 12.917
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3943
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 704

Software

Software
Software Name Purpose
REFMAC refinement version: 5.4.0067
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.000
MAR345 data collection version: CCD
XDS data reduction
SHELXD phasing
autoSHARP phasing