3A3G | pdb_00003a3g

Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-ribityl) lumazine

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	20%(w/v) PEG 4000, 0.2M MgCl2, 100mM Tris-HCl pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.689	α = 90
b = 46.584	β = 90
c = 161.587	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 270		2009-04-28		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.00	Photon Factory	AR-NE3A

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	2	44.766	99.7563				23305

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	MOLECULAR REPLACEMENT	THROUGHOUT	2	44.766	23305	1255	99.76	0.19768	0.19474	0.2	0.2548	0.26	RANDOM	19.594

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]
0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.952
r_dihedral_angle_4_deg	26.767
r_dihedral_angle_3_deg	17.035
r_dihedral_angle_1_deg	8.172
r_scangle_it	4.748
r_scbond_it	2.861
r_mcangle_it	2.07
r_angle_refined_deg	1.733
r_mcbond_it	1.217
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.222
r_chiral_restr	0.153
r_xyhbond_nbd_refined	0.14
r_symmetry_hbond_refined	0.133
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2752
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement