7VIO | pdb_00007vio

Crystal structure of recombinant horse spleen apo-R168H/L169C-Fr

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DAT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	Ammonium Sulfate, Cadmium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.644	α = 90
b = 182.644	β = 90
c = 182.644	γ = 90

Symmetry
Space Group	F 4 3 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		2019-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00	SPring-8	BL45XU

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	1.5	37.31	99.7	0.028	0.039	0.028	0.997	22.7	1.9		42065

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	1.5	1.53			0.039	0.055	0.039	0.995		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	1dat	1.5	37.31	42065	2112	99.586	0.176	0.1751	0.17	0.1934	0.19	14.462

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.575
r_dihedral_angle_4_deg	21.315
r_dihedral_angle_3_deg	12.851
r_lrange_it	5.242
r_dihedral_angle_1_deg	5.14
r_scangle_it	4.311
r_scbond_it	2.992
r_angle_refined_deg	2.217
r_mcangle_it	1.884
r_mcbond_it	1.286
r_nbtor_refined	0.312
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.201
r_symmetry_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.141
r_chiral_restr	0.113
r_metal_ion_refined	0.03
r_symmetry_metal_ion_refined	0.03
r_bond_refined_d	0.015
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1363
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Coot	model building
Aimless	data scaling
MOLREP	phasing