4HYR | pdb_00004hyr

Structure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual static disorder

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	0.1M Bis-Tris pH 5.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.916	α = 90
b = 88.916	β = 90
c = 236.218	γ = 90

Symmetry
Space Group	P 41 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	ADSC QUANTUM 315		2011-06-16		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	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	1.84	50	99.5	0.116	0.079	37.238	23.8	82827	82827			22.4

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	1.84	1.87	90.2		0.97	0.895	3.875	22.4	3700

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	AB INITIO PHASING	THROUGHOUT	1.84	43.69	82357	82357	4129	99.47	0.1647	0.1629	0.1623	0.1997	0.1988	RANDOM	26.0755

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]
-0.06			-0.06		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36
r_dihedral_angle_4_deg	14.455
r_dihedral_angle_3_deg	13.359
r_dihedral_angle_1_deg	5.877
r_angle_refined_deg	1.433
r_angle_other_deg	0.695
r_chiral_restr	0.085
r_gen_planes_refined	0.014
r_bond_refined_d	0.012
r_gen_planes_other	0.002
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6824
Nucleic Acid Atoms
Solvent Atoms	528
Heterogen Atoms	27

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
ARP/wARP	model building
HKL2Map	phasing
PHENIX	phasing