1VM6 | pdb_00001vm6

Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ARZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	4.5	293	20.0% PEG-400, 0.2M Ca(OAc)2, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.077	α = 90
b = 109.217	β = 119.23
c = 112.602	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	ADSC QUANTUM 315	flat mirror	2004-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.27	29.03	47.8	0.086	10.8	3.6		61963			46.59

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	2.27	2.39	38.4		0.507	2	2.5	7228

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	1arz	2.27	29.03	58811	3151	95.49	0.17334	0.17127	0.18	0.21256	0.22	RANDOM	42.509

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]
1.77		-0.6	0.29		-2.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.816
r_dihedral_angle_4_deg	17.957
r_dihedral_angle_3_deg	14.438
r_dihedral_angle_1_deg	5.804
r_scangle_it	5.093
r_scbond_it	3.936
r_mcangle_it	1.742
r_angle_refined_deg	1.596
r_mcbond_it	1.237
r_angle_other_deg	0.919
r_mcbond_other	0.526
r_symmetry_vdw_other	0.205
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.196
r_symmetry_hbond_refined	0.187
r_nbd_other	0.177
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.089
r_nbtor_other	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6730
Nucleic Acid Atoms
Solvent Atoms	529
Heterogen Atoms	275

Software

Software
Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling