2PCE | pdb_00002pce

Crystal structure of putative mandelate racemase/muconate lactonizing enzyme from Roseovarius nubinhibens ISM

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	294	100mM Hepes pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.688	α = 90
b = 174.413	β = 90
c = 108.586	γ = 90

Symmetry
Space Group	P 21 21 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	MAR CCD 165 mm		2007-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	2	121.27	97.7	0.173	0.173	15.6	11.8	209553	209553			27.9

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	2	2.11	91.6		0.821	0.821	2.3	9.5	28399

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2	20	208097	208097	10458	97.06	0.204	0.202	0.2051	0.25	0.2515	RANDOM	35.429

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]
-0.74			-0.91		1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.937
r_dihedral_angle_4_deg	17.815
r_dihedral_angle_3_deg	15.922
r_dihedral_angle_1_deg	9.271
r_scangle_it	3.946
r_scbond_it	2.58
r_angle_refined_deg	1.603
r_mcangle_it	1.498
r_mcbond_it	0.958
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.101
r_symmetry_hbond_refined	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22080
Nucleic Acid Atoms
Solvent Atoms	1001
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
CCP4	data scaling
SHELXD	phasing