X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details 0.2M Calcium chloride, 0.1M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.03 α = 90
b = 83.57 β = 90
c = 63.06 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2008-09-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.42500 LNLS D03B-MX1

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
2.1 83.62 99.9 0.085 0.085 -- 3.4 13519 13519 -- -- --
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)
2.1 2.21 99.9 0.377 0.377 1.9 3.4 1918

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 2.1 21.79 -- 0.0 -- 13517 667 99.96 -- 0.2039 0.2019 0.2436 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 2.1 2.154 -- 45 901 0.244 0.278 -- 99.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.7372
Anisotropic B[1][1] 0.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.15
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.004
r_symmetry_hbond_refined 0.139
r_nbd_refined 0.219
r_chiral_restr 0.069
r_dihedral_angle_1_deg 5.863
r_dihedral_angle_2_deg 34.034
r_xyhbond_nbd_refined 0.165
r_dihedral_angle_3_deg 15.88
r_dihedral_angle_4_deg 16.95
r_angle_refined_deg 1.37
r_bond_refined_d 0.008
r_nbtor_refined 0.311
r_symmetry_vdw_refined 0.304
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1785
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 142

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.25
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.11
MAR345dtb data collection
REFMAC phasing