3B9T | pdb_00003b9t

Crystal structure of predicted acetamidase/formamidase (YP_546212.1) from Methylobacillus flagellatus KT at 1.58 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	NANODROP, 1.0M LiCl, 20.0% PEG 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.165	α = 107.82
b = 82.723	β = 105.81
c = 83.576	γ = 95.18

Symmetry
Space Group	P 1

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	KOHZU: Double crystal Si(111)	2007-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.97960	ALS	8.2.2

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	1.58	29.814	95.8	0.09	0.09	7.2	1.9		196551			13.67

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	1.58	1.62	94.2		0.459	0.459	1.6	1.9	14334

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	1.58	29.814	196547	9907	95.77	0.14	0.138	0.15	0.177	0.19	RANDOM	13.157

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]
0.29	0.25	0.34	0.37	-0.12	-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.972
r_dihedral_angle_4_deg	16.083
r_dihedral_angle_3_deg	11.291
r_dihedral_angle_1_deg	6.464
r_scangle_it	5.052
r_scbond_it	4.01
r_mcangle_it	2.296
r_mcbond_it	1.824
r_angle_refined_deg	1.508
r_angle_other_deg	0.929
r_mcbond_other	0.736
r_symmetry_vdw_other	0.223
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.211
r_nbd_other	0.204
r_nbtor_refined	0.179
r_metal_ion_refined	0.174
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.095
r_nbtor_other	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12906
Nucleic Acid Atoms
Solvent Atoms	1696
Heterogen Atoms	174

Software

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