1VL0 | pdb_00001vl0

CRYSTAL STRUCTURE OF A DTDP-4-DEHYDRORHAMNOSE REDUCTASE, RFBD ORTHOLOG (CA_C2315) FROM CLOSTRIDIUM ACETOBUTYLICUM ATCC 824 AT 2.05 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	0.06M MES, 0.04M MES_Na, 2% NP_PEG MME 2000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	0.06M MES, 0.04M MES_Na, 2% NP_PEG MME 2000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.4
2.62	52.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.8	α = 90
b = 130.67	β = 90
c = 151.05	γ = 90

Symmetry
Space Group	C 2 2 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		2004-03-10	M	SINGLE WAVELENGTH
2	1	x-ray	100	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 8.2.1	0.9795,0.9796	ALS	8.2.1

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	2.05	19.99	99.9	0.076	12.5	4.9		66292			40.95

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	2.05	2.16	100		0.572	2.3	4.8	9628

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	2.05	19.99	63619	2667	99.86	0.17072	0.16921	0.18	0.20701	0.22	RANDOM	38.75

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]
2.66			-0.29		-2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.445
r_dihedral_angle_4_deg	21.169
r_dihedral_angle_3_deg	14.012
r_scangle_it	6.85
r_dihedral_angle_1_deg	5.811
r_scbond_it	5.138
r_mcangle_it	2.779
r_mcbond_it	2.181
r_angle_refined_deg	1.529
r_angle_other_deg	0.953
r_symmetry_vdw_refined	0.322
r_mcbond_other	0.32
r_symmetry_vdw_other	0.279
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.191
r_nbd_other	0.187
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_other	0.11
r_chiral_restr	0.09
r_nbtor_other	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6583
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	149

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing