3I0Z | pdb_00003i0z

Crystal structure of putative putative tagatose-6-phosphate ketose/aldose isomerase (NP_344614.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1860M calcium acetate, 22.2000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.635	α = 90
b = 111.267	β = 97.09
c = 126.6	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-01-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97964	SSRL	BL9-2

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	1.7	29.748	99	0.082	0.082	7.225	2.8		85864			16.104

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	1.7	1.74	98		0.532	0.532	1.4	2.8	6303

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	1.7	29.748	85861	4302	98.87	0.141	0.139	0.1487	0.178	0.1849	RANDOM	20.225

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]
-0.81		0.13	0.46		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.411
r_dihedral_angle_4_deg	16.541
r_dihedral_angle_3_deg	11.772
r_dihedral_angle_1_deg	5.84
r_scangle_it	5.585
r_scbond_it	4.373
r_mcangle_it	2.496
r_mcbond_it	1.982
r_angle_refined_deg	1.521
r_angle_other_deg	0.863
r_mcbond_other	0.572
r_symmetry_vdw_refined	0.442
r_symmetry_vdw_other	0.422
r_symmetry_hbond_refined	0.292
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.207
r_nbd_other	0.2
r_nbtor_refined	0.187
r_chiral_restr	0.097
r_nbtor_other	0.091
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6021
Nucleic Acid Atoms
Solvent Atoms	825
Heterogen Atoms	67

Software

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