4HN0 | pdb_00004hn0

Crystal Structure of ChmJ, a 3'-monoepimerase apoenzyme from Streptomyces bikiniensis

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HMZ	PDB entry 4HMZ

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
3.3	62.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.587	α = 90
b = 141.587	β = 90
c = 115.576	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	ADSC QUANTUM 210r		2012-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	100.12	96		6.7		53594

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	1.8	1.86	89.3		0.43	1.74	2.8	9437

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 4HMZ	2.2	30	53594	2917	97.83	0.21724	0.2149	0.2117	0.25871	0.2552	RANDOM	47.672

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]
0.74			0.74		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.009
r_dihedral_angle_4_deg	21.388
r_dihedral_angle_3_deg	17.764
r_dihedral_angle_1_deg	7.236
r_scangle_it	6.804
r_scbond_it	4.408
r_mcangle_it	2.754
r_angle_refined_deg	2.24
r_mcbond_it	1.559
r_chiral_restr	0.159
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6187
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	52

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling