X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details Protein solution (4.95 mg/ml Protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (0.080 M Calcium chloride, 15% PEG 4000, 0.1 M HEPPS pH 8.5) and cryoprotected with well solution supplemented with 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.46 α = 90
b = 61.99 β = 90
c = 70.02 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER PROTEUM-R MONTEL OPTICS 2007-04-01
Diffraction Radiation
Monochromator Protocol
Graded Multilayer SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 1.5418 -- --

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
1.7 70.2 99.0 0.0976 -- -- 29.45 -- 25086 -- -- --
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)
1.7 1.75 96.8 0.6834 -- 2.93 5.42 2000

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 1.7 46.424 -- 0.0 -- 25028 1276 98.98 -- 0.171 0.168 0.22 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 1.7 1.744 -- 81 1701 0.246 0.323 -- 97.324
X Ray Diffraction 1.744 1.792 -- 93 1626 0.226 0.301 -- 95.873
X Ray Diffraction 1.792 1.844 -- 75 1603 0.215 0.273 -- 96.216
X Ray Diffraction 1.844 1.9 -- 65 1584 0.2 0.241 -- 97.344
X Ray Diffraction 1.9 1.963 -- 83 1540 0.183 0.204 -- 99.024
X Ray Diffraction 1.963 2.031 -- 82 1497 0.163 0.199 -- 100.0
X Ray Diffraction 2.031 2.108 -- 94 1449 0.161 0.26 -- 100.0
X Ray Diffraction 2.108 2.194 -- 73 1425 0.165 0.189 -- 100.0
X Ray Diffraction 2.194 2.291 -- 68 1357 0.161 0.189 -- 100.0
X Ray Diffraction 2.291 2.403 -- 79 1291 0.171 0.22 -- 100.0
X Ray Diffraction 2.403 2.532 -- 75 1227 0.165 0.206 -- 100.0
X Ray Diffraction 2.532 2.685 -- 82 1165 0.165 0.204 -- 100.0
X Ray Diffraction 2.685 2.87 -- 49 1110 0.161 0.292 -- 100.0
X Ray Diffraction 2.87 3.099 -- 61 1038 0.153 0.21 -- 100.0
X Ray Diffraction 3.099 3.393 -- 52 945 0.144 0.216 -- 100.0
X Ray Diffraction 3.393 3.791 -- 42 880 0.133 0.179 -- 99.568
X Ray Diffraction 3.791 4.373 -- 37 785 0.131 0.161 -- 100.0
X Ray Diffraction 4.373 5.344 -- 41 669 0.134 0.175 -- 100.0
X Ray Diffraction 5.344 7.508 -- 29 532 0.204 0.296 -- 99.822
X Ray Diffraction 7.508 46.424 -- 15 328 0.203 0.24 -- 99.133
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.341
Anisotropic B[1][1] 0.312
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.108
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_metal_ion_refined 0.194
r_chiral_restr 0.096
r_scangle_it 3.52
r_dihedral_angle_1_deg 6.337
r_angle_refined_deg 1.548
r_xyhbond_nbd_refined 0.158
r_mcbond_it 0.866
r_nbd_refined 0.235
r_dihedral_angle_2_deg 37.293
r_gen_planes_refined 0.006
r_symmetry_vdw_refined 0.193
r_nbtor_refined 0.303
r_symmetry_hbond_refined 0.23
r_dihedral_angle_4_deg 11.385
r_bond_refined_d 0.012
r_dihedral_angle_3_deg 12.058
r_scbond_it 2.291
r_mcangle_it 1.285
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1915
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 377

Software

Software
Software Name Purpose
SAINT data scaling
MOLREP phasing
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.000
PROTEUM PLUS data collection version: PLUS
SAINT data reduction
SADABS data scaling