X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.43
Temperature 293.0
Details 31.6000% 2-methyl-2,4-pentanediol, 0.2000M sodium chloride, 0.1M sodium acetate pH 4.43, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.8 α = 90
b = 70.34 β = 90
c = 104.1 γ = 90
Symmetry
Space Group I 21 21 21

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) 2009-06-10
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.85503,0.97926,0.97845 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
1.85 29.81 100.0 0.091 0.091 -- 4.1 -- 21313 -- -- 21.528
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)
1.85 1.9 100.0 0.726 0.726 1.0 4.1 1549

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 1.85 29.814 -- 0.0 -- 21310 1095 99.99 -- 0.184 0.182 0.214 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 1.85 1.898 -- 73 1468 0.271 0.304 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.402
Anisotropic B[1][1] -0.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.31
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.642
r_angle_other_deg 0.93
r_mcbond_other 0.277
r_chiral_restr 0.102
r_scangle_it 4.3
r_gen_planes_other 0.001
r_mcbond_it 0.959
r_bond_other_d 0.002
r_bond_refined_d 0.018
r_scbond_it 2.69
r_dihedral_angle_4_deg 17.383
r_gen_planes_refined 0.007
r_angle_refined_deg 1.621
r_dihedral_angle_2_deg 39.549
r_mcangle_it 1.697
r_dihedral_angle_3_deg 14.076
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1729
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 169

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0053
PHENIX refinement
SOLVE phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction