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_symmetry_hbond_refined 0.139
r_bond_refined_d 0.008
r_angle_refined_deg 1.37
r_dihedral_angle_1_deg 5.863
r_dihedral_angle_2_deg 34.034
r_dihedral_angle_3_deg 15.88
r_dihedral_angle_4_deg 16.95
r_chiral_restr 0.069
r_gen_planes_refined 0.004
r_nbd_refined 0.219
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.165
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

Computing
Computing Package Purpose
MAR345dtb Data Collection
mar345dtb Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
refmac Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.2.0019 refinement
SCALA version: 3.2.25 data reduction