X-RAY DIFFRACTION Experimental Data & Validation


Re-refined structure

1 | Text | THIS ENTRY 1SX3 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R1KP8SF DETERMINED BY THE AUTHOR OF THE PDB ENTRY 1KP8: J.WANG | The full text of the PDB remark record.

Done Re-refined structure

Re-refined PDB record

1 | DB record | 1KP8 | The identifying code in the related database. 1ABC BDL001

1 | Detail | THIS ENTRY 1SX3 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R1KP8SF | A description of the related entry. 1ABC contains the same protein complexed with Netropsin.

Done Re-refined PDB Record

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details PEG 8000, bis-tris propane, ethylene glycol, glycerol, potassium chloride, calcium chloride, ATPgammaS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.57 α = 90
b = 260.11 β = 101.14
c = 150.2 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline

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 2.0 39.841 -- 0.0 540790 540790 10647 -- 0.246 0.246 0.2455 0.2647 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 2.0 2.0519 -- 497 24808 0.473 0.464 -- --
X Ray Diffraction 2.052 2.108 -- 534 26914 0.444 0.438 -- --
X Ray Diffraction 2.108 2.1689 -- 615 28836 0.395 0.397 -- --
X Ray Diffraction 2.169 2.2355 -- 575 30010 0.357 0.363 -- --
X Ray Diffraction 2.235 2.3085 -- 639 31203 0.329 0.348 -- --
X Ray Diffraction 2.309 2.3893 -- 614 31929 0.306 0.311 -- --
X Ray Diffraction 2.389 2.4791 -- 656 31948 0.299 0.343 -- --
X Ray Diffraction 2.479 2.58 -- 617 32157 0.282 0.325 -- --
X Ray Diffraction 2.58 2.6942 -- 645 31955 0.263 0.294 -- --
X Ray Diffraction 2.694 2.825 -- 621 31743 0.246 0.266 -- --
X Ray Diffraction 2.825 2.977 -- 589 31214 0.231 0.249 -- --
X Ray Diffraction 2.977 3.1565 -- 623 30548 0.227 0.267 -- --
X Ray Diffraction 3.156 3.3729 -- 591 29503 0.215 0.24 -- --
X Ray Diffraction 3.373 3.641 -- 602 28032 0.217 0.243 -- --
X Ray Diffraction 3.641 3.9852 -- 565 25970 0.211 0.225 -- --
X Ray Diffraction 3.985 4.45 -- 478 23606 0.198 0.22 -- --
X Ray Diffraction 4.45 5.1277 -- 402 20926 0.211 0.234 -- --
X Ray Diffraction 5.128 6.2543 -- 358 17711 0.25 0.268 -- --
X Ray Diffraction 6.254 8.738 -- 284 13558 0.213 0.226 -- --
X Ray Diffraction 8.738 39.841 -- 142 7572 0.216 0.215 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.974
Anisotropic B[1][1] -3.059
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] -0.144
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.206
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.554
r_scbond_it 1.893
r_bond_refined_d 0.026
r_angle_refined_deg 1.961
r_dihedral_angle_1_deg 5.388
r_chiral_restr 0.147
r_gen_planes_refined 0.008
r_xyhbond_nbd_refined 0.159
r_metal_ion_refined 0.357
r_symmetry_vdw_refined 0.428
r_symmetry_hbond_refined 0.417
r_symmetry_metal_ion_refined 0.102
r_mcbond_it 0.624
r_mcangle_it 0.914
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 53970
Nucleic Acid Atoms 0
Heterogen Atoms 464
Solvent Atoms 946

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC 5 (CCP4: Supported Program) version: refmac_5.1.19 refinement