X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.9
Temperature 277.0
Details NANODROP, 0.2M Mg formate, 20.0% PEG 3350, 0.001M Spermine tetra-HCl, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.54 α = 90
b = 36.32 β = 125.46
c = 72.6 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 325 mm CCD Flat mirror (vertical focusing) 2008-02-01
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97922, 0.97874 SSRL BL11-1

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
1.5 25.87 98.3 0.038 -- -- -- -- 30979 -- -3.0 17.062
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)
1.5 1.55 96.7 0.362 -- 2.1 -- --

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 1.5 25.872 -- 0.0 -- 30979 1560 99.56 -- 0.182 0.18 0.217 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 1.5 1.539 -- 109 2152 0.231 0.284 -- 98.56
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.356
Anisotropic B[1][1] -0.75
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.0
Anisotropic B[2][2] 0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 4.39
r_mcbond_it 1.826
r_scangle_it 6.33
r_angle_refined_deg 1.563
r_mcangle_it 2.848
r_angle_other_deg 1.065
r_gen_planes_other 0.002
r_dihedral_angle_3_deg 11.479
r_dihedral_angle_4_deg 13.723
r_mcbond_other 0.527
r_dihedral_angle_1_deg 3.972
r_chiral_restr 0.078
r_bond_other_d 0.001
r_bond_refined_d 0.017
r_dihedral_angle_2_deg 33.877
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1472
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 198

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