3CMB | pdb_00003cmb

Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	277	NANODROP, 30.0% PEG 400, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.34	α = 90
b = 136.71	β = 90
c = 168.12	γ = 90

Symmetry
Space Group	I 2 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-12-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97941, 0.91837, 0.97874	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	29.386	93.1	0.035	14.07			182268		-3	19.237

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.66	71.5		0.413	1.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.6	29.386	182268	9156	93.77	0.229	0.228	0.23	0.259	0.26	RANDOM	16.446

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]
-0.19			0.26		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.464
r_dihedral_angle_4_deg	14.495
r_dihedral_angle_3_deg	13.033
r_dihedral_angle_1_deg	7.33
r_scangle_it	6.537
r_scbond_it	4.742
r_mcangle_it	2.775
r_mcbond_it	2.193
r_angle_refined_deg	1.765
r_angle_other_deg	1.711

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.464
r_dihedral_angle_4_deg	14.495
r_dihedral_angle_3_deg	13.033
r_dihedral_angle_1_deg	7.33
r_scangle_it	6.537
r_scbond_it	4.742
r_mcangle_it	2.775
r_mcbond_it	2.193
r_angle_refined_deg	1.765
r_angle_other_deg	1.711
r_mcbond_other	0.756
r_chiral_restr	0.094
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8496
Nucleic Acid Atoms
Solvent Atoms	1423
Heterogen Atoms	110

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.