4QTG | pdb_00004qtg

CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		0.085M AMMONIUM CITRATE, PH 5.6, 0.17M SODIUM ACETATE, 1MM MNCL2, 25% PEG 4000,15% GLYCEROL, VAPOR DIFFUSION,SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.468	α = 90
b = 85.486	β = 90
c = 141.623	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	CCD	ADSC QUANTUM 315	MIRRORS	2014-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.47	50	97.7	0.102	0.102	18.2	7		122409		-5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.47	1.5	83.1		0.79	0.79	2.1	6.4

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	MR	THROUGHOUT	4QRN	1.47	50	118586	3732	98.14	0.12151	0.12018	0.14	0.16377	0.17	RANDOM	21.901

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]
0.58			-0.26		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.286
r_sphericity_free	25.107
r_dihedral_angle_4_deg	17.151
r_dihedral_angle_3_deg	12.646
r_sphericity_bonded	10.268
r_dihedral_angle_1_deg	6.242
r_scbond_it	5.703
r_scbond_other	5.703
r_scangle_other	5.513
r_rigid_bond_restr	5.242
r_long_range_B_refined	4.624
r_long_range_B_other	4.624
r_mcangle_other	2.752
r_mcangle_it	2.749
r_mcbond_it	2.503
r_mcbond_other	2.496
r_angle_refined_deg	1.77
r_angle_other_deg	1.009
r_chiral_restr	0.128
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5559
Nucleic Acid Atoms
Solvent Atoms	786
Heterogen Atoms	26

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling