6FBM | pdb_00006fbm

Crystal structure of GNIP1Aa from Chromobacterium piscinae

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	100 mM citrate, pH 5.6, 2 % Tacsimate, pH 5.0, 14 % (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.676	α = 90
b = 143.187	β = 90
c = 209.62	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	OXFORD ONYX CCD		2010-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION NOVA	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.5	15	96.6	0.111	0.129	11.9	3.72		79981

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.65	97.7		0.364	0.429		3.58

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	FREE R-VALUE	2.5	14.988	79981	4016	96.675	0.233	0.2304	0.23	0.2714	0.27	27.052

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]
1.331			-0.545		-0.785

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.406
r_dihedral_angle_4_deg	17.21
r_dihedral_angle_3_deg	15.92
r_dihedral_angle_1_deg	6.679
r_lrange_it	5.59
r_lrange_other	5.583
r_scangle_it	3.549
r_scangle_other	3.549
r_mcangle_it	3.389
r_mcangle_other	3.389
r_scbond_it	2.117
r_scbond_other	2.116
r_mcbond_it	2.03
r_mcbond_other	2.029
r_angle_refined_deg	1.55
r_angle_other_deg	0.961
r_symmetry_nbd_refined	0.231
r_nbd_other	0.216
r_symmetry_xyhbond_nbd_refined	0.214
r_nbd_refined	0.19
r_nbtor_refined	0.171
r_symmetry_nbd_other	0.156
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.076
r_ncsr_local_group_6	0.057
r_ncsr_local_group_5	0.056
r_ncsr_local_group_3	0.052
r_ncsr_local_group_2	0.044
r_ncsr_local_group_4	0.043
r_ncsr_local_group_1	0.041
r_symmetry_xyhbond_nbd_other	0.032
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16136
Nucleic Acid Atoms
Solvent Atoms	452
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
CRANK	phasing