9JQW | pdb_00009jqw

The Crystal Structure of LCC6-Active from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M (NH4)2SO4, 0.1M Mes pH6.5, 30% w/v Polyethylene glycol Monomethyl ether 5,000

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.611	α = 90
b = 74.69	β = 90
c = 157.453	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2024-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.979191	SSRF	BL10U2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.05	42.98	99.9	0.194	10.5	10		30250

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11			0.979

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	7vve	2.05	42.979	30188	1489	99.868	0.152	0.1496	0.1639	0.2018	0.2129	20.111

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]
-0.986			-0.016		1.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.53
r_dihedral_angle_3_deg	14.01
r_dihedral_angle_1_deg	6.745
r_lrange_it	5.608
r_dihedral_angle_2_deg	5.425
r_lrange_other	5.295
r_scangle_it	3.746
r_scangle_other	3.745
r_scbond_it	2.469
r_scbond_other	2.468
r_mcangle_it	2.299
r_mcangle_other	2.298
r_mcbond_it	1.524
r_mcbond_other	1.523
r_angle_refined_deg	1.336
r_angle_other_deg	0.451
r_xyhbond_nbd_refined	0.232
r_symmetry_xyhbond_nbd_refined	0.231
r_nbd_refined	0.215
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.178
r_nbd_other	0.172
r_symmetry_nbd_refined	0.154
r_ncsr_local_group_1	0.085
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3840
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	23

Software

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