3LOC | pdb_00003loc

Crystal structure of putative transcriptional regulator ycdc

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	290	SODIUM CHLORIDE, SODIUM FORMATE, GLYCEROL, PH 7, VAPOR DIFFUSION, TEMPERATURE 290K

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.02	α = 90
b = 139.61	β = 90
c = 156	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	200	CCD	SBC-3	MIRRORS	2003-03-11	M	SINGLE WAVELENGTH
2	1	x-ray	200	IMAGE PLATE	MARRESEARCH	MIRRORS	2003-03-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.96367	APS	19-BM
2	SYNCHROTRON	NSLS BEAMLINE X9A	0.972, 0.9786, 0.9789	NSLS	X9A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	50	99.8	0.064	0.093	8	4.48	40218	40218

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	99.3		0.44	0.43	2.1	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.5	49.35	36793	36793	1931	96.21	0.19704	0.19704	0.19537	0.21	0.22905	RANDOM	14.4

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]
0.88			-2.28		1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.838
r_dihedral_angle_4_deg	19.198
r_dihedral_angle_3_deg	17.644
r_dihedral_angle_1_deg	5.267
r_scangle_it	3.132
r_angle_other_deg	2.243
r_scbond_it	2.123
r_angle_refined_deg	1.447
r_mcangle_it	0.944
r_mcbond_it	0.485
r_chiral_restr	0.084
r_mcbond_other	0.08
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6235
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SBC-Collect	data collection
SOLVE	phasing
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
Coot	model building
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing