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 0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5., NANODROP, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.86 α = 90
b = 101.86 β = 90
c = 110.99 γ = 90
Symmetry
Space Group P 41 21 2

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 2008-05-02
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97915,0.97929,0.91162 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
1.8 29.93 100.0 0.114 0.114 -- 7.3 -- 54677 -- -- 17.486
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)
1.8 1.85 100.0 0.558 0.558 1.4 7.3 3969

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 1.8 29.934 -- 0.0 -- 54610 2772 99.96 -- 0.17 0.168 0.208 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 1.8 1.847 -- 167 3800 0.192 0.256 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.944
Anisotropic B[1][1] 0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.72
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.898
r_angle_refined_deg 1.739
r_mcangle_it 2.439
r_bond_other_d 0.002
r_angle_other_deg 1.519
r_gen_planes_other 0.004
r_gen_planes_refined 0.01
r_mcbond_it 1.375
r_bond_refined_d 0.016
r_mcbond_other 0.296
r_dihedral_angle_4_deg 14.327
r_chiral_restr 0.101
r_dihedral_angle_2_deg 32.396
r_dihedral_angle_1_deg 4.605
r_scbond_it 4.089
r_dihedral_angle_3_deg 11.437
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4254
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 680

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PHENIX refinement
SHELX phasing
REFMAC refinement version: 5.4.0067
SCALA data scaling
PDB_EXTRACT data extraction version: 3.004
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing