4HMZ | pdb_00004hmz

Crystal Structure of ChmJ, a 3'-monoepimerase from Streptomyces bikiniensis in complex with dTDP-quinovose

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C0Z	PDB entry 2C0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	20% PEG 3400, 2% 2-methyl-2,4-pentanediol, 100 mM MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.721	α = 90
b = 140.721	β = 90
c = 117.736	γ = 90

Symmetry
Space Group	I 4

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	Bruker Platinum 135	Montel	2012-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	99.5	94.9	0.088		4.2	77282	73347

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1	89.2		0.31	1.95	1.78	9355

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2C0Z	2	30	69652	3693	94.91	0.20165	0.19911	0.2012	0.24883	0.2496	RANDOM	23.47

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]
0.11			0.11		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.638
r_dihedral_angle_4_deg	19.517
r_dihedral_angle_3_deg	16.528
r_dihedral_angle_1_deg	6.729
r_scangle_it	5.468
r_scbond_it	3.659
r_mcangle_it	2.233
r_angle_refined_deg	2.217
r_mcbond_it	1.366
r_chiral_restr	0.147
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6242
Nucleic Acid Atoms
Solvent Atoms	385
Heterogen Atoms	168

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling