X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 295.0
Details 11 mg/mL protein incubated with 4 mM inhibitor at 4C overnight followed by addition of 1 ug Arg-C (per 50 ul sample) at 22C for 24 hours, followed by addition of 0.5 uL of 5 mg/mL leupeptin, followed by mixing with equal volumes of well solution:22.5-35% PEG 4000, 0.1M Tris-HCL pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.92 α = 90
b = 62.92 β = 90
c = 183.94 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-04-09
Diffraction Radiation
Monochromator Protocol
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.07816 APS 21-ID-D

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
3.4 20 95.2 -- 0.156 -- 3.2 5300 5285 -- -3.0 68.0
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)
3.4 3.52 98.5 -- 0.579 1.9 3.3 536

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 3.4 19.9 -3.0 0.0 5300 5035 250 95.59 0.247 0.24721 0.24518 0.28882 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 3.401 3.487 -- 23 364 0.299 0.329 -- 97.48
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 62.589
Anisotropic B[1][1] 1.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.4
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.041
r_bond_refined_d 0.004
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 4.163
r_mcangle_it 0.072
r_angle_refined_deg 0.713
r_gen_planes_refined 0.002
r_bond_other_d 0.001
r_mcbond_it 0.038
r_dihedral_angle_2_deg 33.017
r_angle_other_deg 0.721
r_scbond_it 0.072
r_dihedral_angle_4_deg 15.613
r_dihedral_angle_3_deg 12.463
r_scangle_it 0.128
r_mcbond_other 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2252
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 0

Software

Software
Software Name Purpose
HKL-2000 data collection
REFMAC refinement version: rigid body refinement
HKL-2000 data reduction
HKL-2000 data scaling
REFMAC phasing version: rigid body refinement