1VRB | pdb_00001vrb

Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP		293	24% NP_PEG 4000, 0.065M Tris_base, 0.16M Mg Cl, 0.035M Tris Cl, 20% Glycerol, CuCl2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
2	VAPOR DIFFUSION, SITTING DROP, NANODROP		293	24% NP_PEG 4000, 0.065M Tris_base, 0.16M Mg Cl, 0.035M Tris Cl, 20% Glycerol, CuCl2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.49
2.8	55.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.3	α = 90
b = 104.66	β = 90
c = 286.61	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		2003-09-22	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC		2003-09-11	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.979686, 0.979835, 1.020026	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	28.66	98.6	0.067	13.7	4.6		49807			82.46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.5	2.64	93.3		0.727	2.3	3	6756

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	2.6	28.66	42483	2243	99.3	0.22399	0.22144	0.22	0.27227	0.27	RANDOM	62.826

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]
6			-1.49		-4.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.594
r_dihedral_angle_4_deg	20.523
r_dihedral_angle_3_deg	19.325
r_dihedral_angle_1_deg	7.582
r_scangle_it	5.77
r_scbond_it	4.206
r_mcangle_it	2.341
r_angle_refined_deg	1.595
r_mcbond_it	1.535
r_angle_other_deg	0.873
r_mcbond_other	0.492
r_nbd_refined	0.248
r_symmetry_vdw_other	0.202
r_nbtor_refined	0.199
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.145
r_symmetry_vdw_refined	0.129
r_nbtor_other	0.092
r_chiral_restr	0.085
r_xyhbond_nbd_other	0.019
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9010
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHELXD	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
autoSHARP	phasing