X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 277.0
Details 0.2000M NaCl, 50.0000% PEG-200, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.21 α = 90
b = 59.37 β = 103.27
c = 61.33 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) 2009-03-27
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 0.97860,0.91837,0.97985 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
1.79 41.52 97.1 0.111 -- -- -- -- 31085 -- -3.0 16.976
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)
1.78 1.84 86.2 0.771 -- 1.8 -- --

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 1.79 41.523 -- 0.0 -- 31083 1564 97.98 -- 0.165 0.163 0.197 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 1.786 1.833 -- 119 2083 0.25 0.279 -- 94.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.859
Anisotropic B[1][1] -0.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.5
Anisotropic B[2][2] -0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.64
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.571
r_angle_other_deg 0.914
r_mcbond_it 1.823
r_scangle_it 6.708
r_bond_other_d 0.001
r_angle_refined_deg 1.499
r_gen_planes_refined 0.008
r_chiral_restr 0.089
r_gen_planes_other 0.001
r_bond_refined_d 0.015
r_dihedral_angle_3_deg 12.889
r_dihedral_angle_1_deg 6.563
r_dihedral_angle_4_deg 21.671
r_mcangle_it 2.866
r_scbond_it 4.588
r_dihedral_angle_2_deg 31.371
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2409
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 265

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0053
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
SHELXD phasing
autoSHARP phasing