8QBJ | pdb_00008qbj

Structure of mBaoJin at pH 4.6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8Q79

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	PEG3350, 0.2 M lithium sulfate, 0.1 M Na Acetate pH4.6

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.447	α = 90
b = 78.919	β = 90
c = 84.434	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	RIGAKU HyPix-6000HE		2023-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU MICROMAX-003	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.8	25	99.6	0.99	6.98	3.2		41116

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.87			0.63

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	15	36375	1822	86.978	0.203	0.1986	0.21	0.2845	0.29	19.953

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]
-0.207			2.152		-1.945

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.652
r_dihedral_angle_4_deg	19.105
r_dihedral_angle_3_deg	17.778
r_dihedral_angle_1_deg	9.264
r_lrange_it	6.623
r_lrange_other	6.402
r_scangle_it	4.455
r_scangle_other	4.455
r_mcangle_other	3.32
r_mcangle_it	3.319
r_scbond_it	3.062
r_scbond_other	3.061
r_mcbond_it	2.401
r_mcbond_other	2.397
r_angle_refined_deg	2.273
r_angle_other_deg	1.463
r_nbd_other	0.387
r_symmetry_xyhbond_nbd_refined	0.354
r_xyhbond_nbd_refined	0.329
r_symmetry_nbd_refined	0.326
r_nbd_refined	0.229
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_other	0.166
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.015
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3443
Nucleic Acid Atoms
Solvent Atoms	655
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing