1VKM | pdb_00001vkm

Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.4	277	7% PEG 1000, 0.045M HEPES_Na, 0.055M HEPES, 0.01M MANGANESE (II) CHLORIDE, pH 7.4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.36
2	37.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.958	α = 90
b = 130.799	β = 90
c = 138.75	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		2003-10-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC		2003-10-12	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 8.2.2	1.0000, 0.9797, 0.9795	ALS	8.2.2

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	1.9	75.23	99.1	0.063	13.7	4.7		130700			32.57

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	1.9	1.95	93.3		0.533	1.9	2.8	9022

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	1.9	75.23	124050	6577	98.93	0.15618	0.15384	0.17	0.19959	0.21	RANDOM	24.631

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]
-0.14			-0.64		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.363
r_dihedral_angle_4_deg	21.165
r_dihedral_angle_3_deg	13.69
r_scangle_it	7.294
r_dihedral_angle_1_deg	5.839
r_scbond_it	5.308
r_mcangle_it	2.688
r_mcbond_it	2.058
r_angle_refined_deg	1.514
r_angle_other_deg	0.846
r_mcbond_other	0.668
r_symmetry_vdw_other	0.259
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.189
r_nbd_other	0.175
r_symmetry_vdw_refined	0.168
r_chiral_restr	0.089
r_nbtor_other	0.083
r_xyhbond_nbd_refined	0.053
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13623
Nucleic Acid Atoms
Solvent Atoms	984
Heterogen Atoms	138

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
SHARP	phasing
REFMAC	refinement
CCP4	data scaling