X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details Protein solution (10 mg/ml protein, 0.10 M Bis Tris, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, pH 7.0) mixed in a 1:1 ratio with the well solution (24% MEPEG 5K, 0.05 M magnesium sulfate, 0.1 M HEPPS pH 8.5),temperature 277K, vapor diffusion, hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.86 α = 90
b = 114.5 β = 90
c = 190.92 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-10-10
Diffraction Radiation
Monochromator Protocol
-- --
CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.97911, 0.96403 APS 22-ID

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 42.57 95.1 0.091 -- -- 6.8 -- 52961 -- -- --
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 1.76 73.4 0.232 -- 4.373 4.8 4054

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 1.702 42.57 -- -- -- 52917 2669 95.086 0.173 0.17331 0.1712 0.2139 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 1.702 1.746 -- 130 2762 0.222 0.262 -- 71.958
X Ray Diffraction 1.746 1.794 -- 191 3010 0.208 0.257 -- 80.468
X Ray Diffraction 1.794 1.846 -- 180 3156 0.203 0.256 -- 86.988
X Ray Diffraction 1.846 1.902 -- 162 3391 0.194 0.233 -- 93.945
X Ray Diffraction 1.902 1.965 -- 186 3342 0.188 0.241 -- 97.891
X Ray Diffraction 1.965 2.034 -- 176 3351 0.191 0.239 -- 99.774
X Ray Diffraction 2.034 2.11 -- 172 3236 0.181 0.231 -- 99.971
X Ray Diffraction 2.11 2.197 -- 184 3112 0.185 0.235 -- 100.0
X Ray Diffraction 2.197 2.294 -- 157 3019 0.182 0.207 -- 100.0
X Ray Diffraction 2.294 2.406 -- 158 2826 0.181 0.23 -- 100.0
X Ray Diffraction 2.406 2.536 -- 133 2737 0.183 0.26 -- 100.0
X Ray Diffraction 2.536 2.69 -- 128 2591 0.185 0.222 -- 99.963
X Ray Diffraction 2.69 2.876 -- 134 2443 0.179 0.222 -- 100.0
X Ray Diffraction 2.876 3.106 -- 107 2275 0.175 0.224 -- 99.874
X Ray Diffraction 3.106 3.402 -- 111 2102 0.156 0.207 -- 99.91
X Ray Diffraction 3.402 3.803 -- 97 1913 0.145 0.194 -- 99.851
X Ray Diffraction 3.803 4.39 -- 90 1702 0.133 0.174 -- 100.0
X Ray Diffraction 4.39 5.373 -- 76 1446 0.141 0.16 -- 99.934
X Ray Diffraction 5.373 7.587 -- 59 1171 0.183 0.188 -- 100.0
X Ray Diffraction 7.587 95.346 -- 38 663 0.181 0.215 -- 98.872
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.484
Anisotropic B[1][1] -0.098
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.633
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.535
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.168
r_dihedral_angle_4_deg 13.478
r_nbtor_refined 0.307
r_xyhbond_nbd_refined 0.141
r_gen_planes_refined 0.006
r_mcbond_it 1.277
r_scangle_it 4.643
r_chiral_restr 0.097
r_symmetry_vdw_refined 0.179
r_scbond_it 3.331
r_dihedral_angle_2_deg 34.949
r_dihedral_angle_3_deg 13.121
r_bond_refined_d 0.014
r_angle_refined_deg 1.392
r_nbd_refined 0.198
r_dihedral_angle_1_deg 5.608
r_mcangle_it 2.096
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3853
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 633

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
DM phasing version: 5.0
REFMAC refinement version: refmac_5.2.0005
PDB_EXTRACT data extraction version: 1.701
PHENIX phasing
SHELXD phasing
SOLOMON phasing
ARP/wARP model building