9BWU | pdb_00009bwu

Glutarate L-2-hydroxylase (CsiD/GlaH) from Escherichia coli at 2.20 Angstroms Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R6S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.2 M Potassium citrate tribasic monohydrate, 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.83	α = 90
b = 123.83	β = 90
c = 139.03	γ = 90

Symmetry
Space Group	I 4 2 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	CCD	RAYONIX MX-300		2022-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.2	61.92	94	0.109	0.127	0.064	0.995	11.3	7.2		26092			20.33

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	2.2	2.27	71.8		0.328	0.382	0.196	0.934	5	7.3

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	2.2	61.915	26089	1359	94.045	0.192	0.1904	0.1903	0.2258	0.2257	Random selection	22.962

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]
0.046			0.046		-0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.46
r_dihedral_angle_3_deg	13.809
r_dihedral_angle_2_deg	10.702
r_lrange_it	8.364
r_scangle_it	6.779
r_dihedral_angle_1_deg	6.299
r_scbond_it	4.6
r_mcangle_it	4.033
r_mcbond_it	2.825
r_angle_refined_deg	1.979
r_nbtor_refined	0.306
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.144
r_chiral_restr	0.096
r_symmetry_xyhbond_nbd_refined	0.095
r_bond_refined_d	0.017
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2373
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	1

Software

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