7CBU | pdb_00007cbu

Blasnase-T13A with L-Asp

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7C91

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	formate

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.651	α = 90
b = 92.651	β = 90
c = 234.096	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9791	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	2.25	19.925	99.9	0.041	0.999	12.3	24.6		49335

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.32			0.408	0.724	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7C91	2.25	19.925	49244	2380	99.785	0.197	0.1964	0.2	0.2169	0.22	43.808

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.277			1.277		-2.554

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.721
r_dihedral_angle_4_deg	20.274
r_dihedral_angle_3_deg	15.568
r_lrange_other	5.73
r_lrange_it	5.729
r_dihedral_angle_1_deg	5.706
r_scangle_it	4.92
r_scangle_other	4.919
r_mcangle_it	3.861
r_mcangle_other	3.861
r_scbond_other	3.792
r_scbond_it	3.791
r_mcbond_it	3.004
r_mcbond_other	3.003
r_angle_other_deg	2.311
r_angle_refined_deg	1.702
r_symmetry_nbd_other	0.22
r_symmetry_xyhbond_nbd_other	0.214
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.188
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.181
r_nbd_other	0.181
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.076
r_metal_ion_refined	0.051
r_bond_other_d	0.036
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4897
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing