2P8G | pdb_00002p8g

Crystal structure of phenolic acid decarboxylase (2635953) from Bacillus subtilis at 1.36 A resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CG9	PDB entry 2CG9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	NANODROP, 0.2M NaCl, 10.0% PEG 8000, 1.0M LiCl, 20.0% PEG 6000, 0.1M Na,K Phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.475	α = 90
b = 117.475	β = 90
c = 117.475	γ = 90

Symmetry
Space Group	P 41 3 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	ADSC QUANTUM 315		2006-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.00000	ALS	5.0.3

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	1.36	58.722	99.6	0.107	0.107	5.6	18.2		59580

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	1.36	1.43	97.4		0.01	1.036	0.7	8.1	8323

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 (All)	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	PDB entry 2CG9	1.36	58.722	59375	2999	99.35	0.134	0.134	0.133	0.15	0.146	0.16	RANDOM	14.486

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.902
r_dihedral_angle_4_deg	14.996
r_dihedral_angle_3_deg	10.437
r_dihedral_angle_1_deg	6.828
r_scangle_it	5.662
r_scbond_it	3.713
r_mcangle_it	2.135
r_mcbond_it	1.666
r_angle_refined_deg	1.489
r_angle_other_deg	0.847
r_mcbond_other	0.353
r_symmetry_vdw_other	0.278
r_symmetry_vdw_refined	0.23
r_nbd_other	0.21
r_nbd_refined	0.203
r_nbtor_refined	0.197
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.093
r_nbtor_other	0.093
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1348
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	32

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing