9RVF | pdb_00009rvf

Structure of Bgla9 from Anoxybacillus ayderensis

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AHX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	20%w/v PEG4000, 20%v/v 2-Propanol, 0.1 M Na citrate pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.088	α = 90
b = 90.733	β = 90
c = 92.103	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		2024-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.6	51.5	92.4	0.082	0.087	0.024	0.999	14.7	11.2		61852

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	1.6	1.65	56.6		1.832	2.075	0.955	0.323	0.3	4.5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	51.5	61784	2094	92.4	0.175	0.1732	0.1681	0.2138	0.2075	Random selection	32.148

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]
0.44			-0.836		0.396

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.938
r_dihedral_angle_3_deg	14.527
r_dihedral_angle_2_deg	9.593
r_dihedral_angle_1_deg	6.751
r_lrange_it	6.419
r_lrange_other	6.414
r_scangle_it	5.122
r_scangle_other	5.121
r_scbond_it	3.52
r_scbond_other	3.519
r_mcangle_it	2.365
r_mcangle_other	2.364
r_angle_refined_deg	2.239
r_mcbond_it	1.913
r_mcbond_other	1.91
r_angle_other_deg	0.797
r_metal_ion_refined	0.337
r_nbd_refined	0.242
r_nbtor_refined	0.195
r_symmetry_nbd_other	0.191
r_symmetry_nbd_refined	0.179
r_nbd_other	0.175
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.126
r_symmetry_xyhbond_nbd_refined	0.09
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.055
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3716
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	5

Software

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