X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 1.1M Malonic Acid, 0.15 M Ammonium Citrate Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic, Final pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.91 α = 118.59
b = 132.29 β = 96.39
c = 131.54 γ = 96.27
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2013-01-18
Diffraction Radiation
Monochromator Protocol
-- SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
2.68 50 94.9 0.067 -- -- 1.9 -- 67209 -- -- --
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)
2.7 2.75 90.9 0.629 -- -- 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
MOLECULAR REPLACEMENT 2.68 38.04 -- -- -- 53394 3007 79.53 -- 0.16832 0.16549 0.216 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 2.685 2.754 -- 13 338 0.196 0.277 -- 6.64
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 122.84
Anisotropic B[1][1] -33.08
Anisotropic B[1][2] -1.5
Anisotropic B[1][3] -4.37
Anisotropic B[2][2] 74.15
Anisotropic B[2][3] -12.52
Anisotropic B[3][3] -41.07
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 53.84
r_rigid_bond_restr 8.222
r_scbond_it 1.995
r_mcangle_it 3.878
r_mcbond_it 2.263
r_gen_planes_refined 0.006
r_chiral_restr 0.094
r_dihedral_angle_4_deg 18.677
r_dihedral_angle_3_deg 18.936
r_dihedral_angle_2_deg 38.809
r_dihedral_angle_1_deg 7.51
r_angle_refined_deg 1.421
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6006
Nucleic Acid Atoms 5357
Heterogen Atoms 0
Solvent Atoms 69

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.5.1 molecular replacement
SCALEPACK data reduction