2QE8 | pdb_00002qe8

Crystal structure of a putative hydrolase (ava_4197) from anabaena variabilis atcc 29413 at 1.35 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	277	NANODROP, 0.8M K2HPO4, 0.2M Li2SO4, 1.2M NaH2PO4, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	6	277	NANODROP, 1.6M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.831	α = 90
b = 135.562	β = 90
c = 51.519	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	ADSC QUANTUM 4	1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing	2007-06-06	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2007-06-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.980910	SSRL	BL1-5
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97929, 0.89194, 0.97905	SSRL	BL9-2

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	1.35	29.348	95.9	0.052	0.052	8.2	4.8		170743			13.57

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	1.35	1.39	73.9		0.346	0.346	1.1	2.1	9561

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	1.35	29.348	170682	8613	95.79	0.117	0.116	0.13	0.144	0.15	RANDOM	13.292

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]
0.28			-0.75		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.588
r_dihedral_angle_4_deg	11.679
r_dihedral_angle_3_deg	11.322
r_sphericity_free	10.036
r_dihedral_angle_1_deg	6.868
r_scangle_it	5.857
r_sphericity_bonded	4.969
r_scbond_it	4.604
r_mcangle_it	3.711
r_mcbond_it	2.836
r_rigid_bond_restr	2.16
r_mcbond_other	1.923
r_angle_refined_deg	1.644
r_angle_other_deg	1.021
r_symmetry_vdw_refined	0.298
r_symmetry_vdw_other	0.246
r_xyhbond_nbd_refined	0.231
r_nbd_refined	0.229
r_nbd_other	0.205
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.17
r_chiral_restr	0.109
r_nbtor_other	0.088
r_bond_refined_d	0.016
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	5178
Nucleic Acid Atoms
Solvent Atoms	833
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing