X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 295.0
Details 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE pH 5.6, 1.3M LITHIUM SULFATE, 0.3M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 144.19 α = 90
b = 144.19 β = 90
c = 69.87 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2011-11-08
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.461 LNLS W01B-MX2

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
1.56 22.43 99.9 0.077 0.077 -- 8.8 116828 116828 -- 2.5 17.9
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)
1.56 1.65 99.9 0.218 0.218 7.8 7.8 16994

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 1.56 22.43 -- -- 110920 110920 5843 99.84 -- 0.17726 0.17639 0.19352 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 1.563 1.603 -- 410 7985 0.271 0.288 -- 99.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.43
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.007
r_chiral_restr 0.085
r_dihedral_angle_4_deg 14.545
r_dihedral_angle_3_deg 11.247
r_dihedral_angle_2_deg 40.094
r_dihedral_angle_1_deg 5.878
r_angle_refined_deg 1.275
r_bond_refined_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4731
Nucleic Acid Atoms 0
Heterogen Atoms 114
Solvent Atoms 608

Software

Computing
Computing Package Purpose
NatXray software Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
MOLREP model building
NatXray version: software data collection