X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.33
Temperature 277.0
Details NANODROP, 7.5% PEG 8000, 36.0% 2-methyl-2,4-pentanediol, 0.1M Sodium cacodylate pH 6.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 273.72 α = 90
b = 158.56 β = 116.03
c = 181.24 γ = 90
Symmetry
Space Group C 1 2 1

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) 2007-02-24
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97935 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 48.56 93.7 0.072 -- -- 2.83 -- 437594 -- -- 25.43
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)
2.0 2.11 72.2 0.442 -- 2.39 2.58 45786

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, MAD 2.0 48.564 -- 0.0 -- 437582 5300 97.54 0.149 0.149 0.148 0.178 THIN SHELLS
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 2.0 2.052 -- -- 22694 0.228 -- -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.506
Anisotropic B[1][1] 0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.89
Anisotropic B[2][2] 1.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.35
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.199
r_nbtor_refined 0.182
r_gen_planes_other 0.001
r_symmetry_vdw_refined 0.101
r_dihedral_angle_2_deg 34.084
r_nbtor_other 0.084
r_scbond_it 4.786
r_angle_other_deg 0.955
r_nbd_refined 0.214
r_scangle_it 6.513
r_mcbond_it 1.33
r_angle_refined_deg 1.388
r_metal_ion_refined 0.091
r_chiral_restr 0.088
r_symmetry_hbond_refined 0.156
r_dihedral_angle_4_deg 16.81
r_mcbond_other 0.495
r_bond_refined_d 0.015
r_bond_other_d 0.002
r_symmetry_vdw_other 0.301
r_gen_planes_refined 0.006
r_xyhbond_nbd_refined 0.186
r_dihedral_angle_3_deg 13.025
r_mcangle_it 2.382
r_dihedral_angle_1_deg 6.215
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 41334
Nucleic Acid Atoms 0
Heterogen Atoms 327
Solvent Atoms 3732

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
SHELX phasing
REFMAC refinement version: 5.2.0019
XSCALE data scaling
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: CCD
XDS data reduction
MOLREP phasing
SHELXD phasing
autoSHARP phasing