6JVV | pdb_00006jvv

Crystal structure of maleylpyruvate hydrolase from Sphingobium.sp SYK-6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PFZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG3350, Lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.089	α = 90
b = 74.519	β = 118.56
c = 67.967	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 270		2018-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	50	97.4	0.054	0.058	0.023	13	6.2		91240

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	61.1		0.35	0.398	0.185	0.807		4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4PFZ	1.51	31.63	86720	4511	98.92	0.1526	0.1515	0.1632	0.1737	0.186	RANDOM	19.236

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]
-0.83		-0.32	-0.24		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.238
r_dihedral_angle_4_deg	19.159
r_dihedral_angle_3_deg	12.835
r_dihedral_angle_1_deg	6.718
r_angle_refined_deg	1.934
r_angle_other_deg	1.506
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3976
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	66

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-2000	data reduction