5R62 | pdb_00005r62

PanDDA analysis group deposition -- Crystal Structure of FIBRINOGEN-LIKE GLOBE DOMAIN OF HUMAN TENASCIN-C in complex with Z2856434840

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6QNV	6QNV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	MORPHEUS 0.09M NPS, 0.1M BUFFER SYSTEM 3 PH = 8.5, 50% V/V PRECIPITANT MIX 1

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.223	α = 90
b = 77.223	β = 90
c = 71.785	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		2019-05-20		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.4	54.6	99.8	0.065	0.068	0.02	1	16.2	10.8		43390

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.47	98.8		1.977	2.141	0.797	0.53		6.9	6148

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6QNV	1.4	54.6	40901	2013	98.79	0.19	0.1884	0.1943	0.2218	0.2278	RANDOM	22.753

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]
1.05			1.05		-2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.803
r_dihedral_angle_4_deg	15.113
r_dihedral_angle_3_deg	12.57
r_dihedral_angle_1_deg	7.33
r_mcangle_it	3.041
r_mcbond_it	2.062
r_mcbond_other	2.061
r_angle_refined_deg	1.828
r_angle_other_deg	1.586
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1677
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing