9JP7 | pdb_00009jp7

4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni (strain DSM 14576 / KF-1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	300	0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3,350.

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.045	α = 90
b = 270.201	β = 90
c = 113.627	γ = 90

Symmetry
Space Group	C 2 2 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		2022-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	3.05	26.44	98.3	0.978	6.3	4.8		37226

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	3.05	3.19			0.911

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	3.05	25.221	37214	1829	98.063	0.267	0.2635	0.2652	0.3352	0.3379	30.756

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]
-1.901			2.143		-0.242

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.832
r_dihedral_angle_6_deg	14.327
r_dihedral_angle_2_deg	9.462
r_dihedral_angle_1_deg	7.584
r_lrange_it	6.815
r_rigid_bond_restr	3.979
r_scangle_it	3.482
r_mcangle_it	3.409
r_scbond_it	2.154
r_mcbond_it	2.111
r_angle_refined_deg	1.496
r_nbtor_refined	0.318
r_nbd_refined	0.239
r_symmetry_nbd_refined	0.236
r_xyhbond_nbd_refined	0.142
r_ncsr_local_group_3	0.112
r_chiral_restr	0.111
r_ncsr_local_group_5	0.109
r_ncsr_local_group_6	0.105
r_ncsr_local_group_1	0.093
r_ncsr_local_group_2	0.084
r_ncsr_local_group_4	0.078
r_symmetry_xyhbond_nbd_refined	0.045
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10283
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	4

Software

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