X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 291.0
Details 10 ul drops with 6-8 mg/ml protein, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) pH 7.5, 50 mM, sodium acetate pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5%(v/v) glycerol, 2%(w/v) PEG 4000, and 0.3-0.5 mM 3-chloromercuri-2-methoxypropylurea suspended over 1 ml of a resevoir solution: 50 mM ADA pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5%(v/v) MPD, 10%(v/v) glycerol, and 8-10%(w/v) PEG 4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.87 α = 90
b = 149.55 β = 90
c = 79.39 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2011-11-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
1.69 74.74 96.4 0.041 -- -- 5.54 -- 34359 -- -- --
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)
1.69 1.75 93.1 0.232 -- 5.3 4.64 3247

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
MOLECULAR REPLACEMENT 1.69 74.74 -- 0.0 -- 32631 1728 96.29 -- 0.1789 0.1774 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 1.69 1.734 -- 127 2278 0.271 0.324 -- 92.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.229
Anisotropic B[1][1] -0.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.91
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 14.149
r_dihedral_angle_1_deg 6.353
r_mcangle_it 3.076
r_chiral_restr 0.106
r_gen_planes_refined 0.009
r_bond_other_d 0.001
r_angle_refined_deg 1.674
r_mcbond_it 2.132
r_dihedral_angle_4_deg 21.466
r_angle_other_deg 0.861
r_mcbond_other 2.132
r_bond_refined_d 0.014
r_dihedral_angle_2_deg 33.08
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2126
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 185

Software

Software
Software Name Purpose
d*TREK data scaling version: 9.4SSI
REFMAC refinement version: 5.8.0073
PDB_EXTRACT data extraction version: 3.15
CrystalClear data reduction
PHASER phasing