2QJ8 | pdb_00002qj8

Crystal structure of an aspartoacylase family protein (mlr6093) from mesorhizobium loti maff303099 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	NANODROP, 20.0% PEG 3350, 0.2M Potassium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.054	α = 90
b = 86.14	β = 90
c = 94.632	γ = 90

Symmetry
Space Group	P 21 21 21

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	2007-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.978662	SSRL	BL1-5

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	29.643	99.8	0.105	0.105	11.5	4.6		45402			26.79

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	2.05	98.7		0.782	0.782	1.7	3.8	3268

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	SAD	THROUGHOUT	2	29.643	45330	2286	99.77	0.209	0.207	0.21	0.254	0.26	RANDOM	24.569

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]
-1.57			-0.25		1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.683
r_dihedral_angle_3_deg	11.336
r_dihedral_angle_4_deg	11.075
r_scangle_it	5.896
r_scbond_it	4.346
r_dihedral_angle_1_deg	4.003
r_mcangle_it	2.53
r_mcbond_it	1.792
r_angle_refined_deg	1.786
r_angle_other_deg	1.367
r_mcbond_other	0.663
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.169
r_nbd_refined	0.165
r_nbtor_refined	0.16
r_nbd_other	0.149
r_symmetry_vdw_other	0.133
r_chiral_restr	0.103
r_nbtor_other	0.082
r_symmetry_vdw_refined	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4499
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms

Software

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