X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.33
Temperature 293.0
Details 45.5% polyethylene glycol 600, 0.1M phosphate-citrate pH 4.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.97 α = 90
b = 103.97 β = 90
c = 59.87 γ = 90
Symmetry
Space Group P 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2010-07-22
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97903,0.97922,0.91837 SSRL BL9-2

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
1.81 46.5 100.0 0.122 -- -- -- -- 58472 -- -3.0 20.884
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)
1.81 1.87 100.0 0.689 -- 2.2 -- --

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 1.81 46.496 -- 0.0 -- 58470 2956 99.96 -- 0.1679 0.1661 0.2017 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 1.81 1.857 -- 183 4149 0.257 0.321 -- 99.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.3316
Anisotropic B[1][1] 0.78
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.56
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.46
r_mcangle_it 2.598
r_dihedral_angle_4_deg 14.472
r_dihedral_angle_1_deg 6.413
r_chiral_restr 0.083
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 11.866
r_dihedral_angle_2_deg 32.4
r_scbond_it 4.052
r_mcbond_it 1.616
r_bond_other_d 0.001
r_angle_other_deg 0.808
r_bond_refined_d 0.014
r_mcbond_other 0.506
r_scangle_it 5.769
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3852
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 455

Software

Software
Software Name Purpose
SHELX phasing
REFMAC refinement version: 5.5.0110
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.10
XDS data reduction
SHELXD phasing
autoSHARP phasing