X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 277.0
Details 0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.69 α = 90
b = 63.34 β = 90
c = 82.06 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-05-14
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97956,0.97904 SSRL BL11-1

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
2.3 29.57 95.9 0.097 -- -- 3.63 -- 13596 -- -3.0 34.972
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)
2.3 2.38 90.5 0.571 -- 1.58 -- --

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 2.3 29.566 -- 0.0 -- 13568 677 97.56 -- 0.219 0.217 0.269 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 2.299 2.38 -- 58 1225 0.263 0.289 -- 96.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.26
Anisotropic B[1][1] 2.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.92
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.225
r_nbtor_other 0.087
r_dihedral_angle_4_deg 10.103
r_dihedral_angle_3_deg 13.55
r_angle_other_deg 0.839
r_nbtor_refined 0.172
r_bond_refined_d 0.009
r_angle_refined_deg 1.073
r_xyhbond_nbd_refined 0.142
r_bond_other_d 0.006
r_dihedral_angle_1_deg 4.557
r_nbd_refined 0.192
r_nbd_other 0.17
r_mcbond_it 1.304
r_scbond_it 3.402
r_gen_planes_other 0.001
r_gen_planes_refined 0.003
r_symmetry_vdw_refined 0.105
r_symmetry_hbond_refined 0.243
r_chiral_restr 0.065
r_mcangle_it 2.082
r_mcbond_other 0.211
r_dihedral_angle_2_deg 33.959
r_scangle_it 4.632
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2288
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 98

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.004
XDS data reduction
SHELXD phasing
autoSHARP phasing