3H08 | pdb_00003h08

Crystal structure of the Ribonuclease H1 from Chlorobium tepidum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	20% PEG 4000, 0.1M sodium HEPES, 10% ispropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2	VAPOR DIFFUSION, HANGING DROP	5.4	298	26% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.457	α = 100.38
b = 33.388	β = 99.43
c = 66.072	γ = 90.82

Symmetry
Space Group	P 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	MARMOSAIC 325 mm CCD		2005-05-22	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2005-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	1.1158	SSRL	BL11-1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.9794	ALS	8.3.1

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	1.6	50	95.5	0.046	23.3		36214	36214

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)
	1.6	1.66	92.8		0.093	8.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.6	50	36214	33439	1758	95.52	0.16146	0.15969	0.23	0.19362	0.25	RANDOM	23.484

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]
0.33	-1.07	-0.3	0.76	-0.57	-1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.664
r_dihedral_angle_4_deg	23.657
r_dihedral_angle_3_deg	13.941
r_sphericity_free	8.707
r_dihedral_angle_1_deg	6.65
r_scangle_it	4.461
r_scbond_it	3.259
r_sphericity_bonded	2.442
r_mcangle_it	2.001
r_mcbond_it	1.677
r_rigid_bond_restr	1.55
r_angle_refined_deg	1.32
r_angle_other_deg	0.715
r_mcbond_other	0.519
r_symmetry_vdw_other	0.294
r_symmetry_hbond_refined	0.289
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.225
r_symmetry_vdw_refined	0.225
r_metal_ion_refined	0.211
r_nbd_other	0.194
r_xyhbond_nbd_other	0.187
r_nbtor_refined	0.183
r_chiral_restr	0.09
r_nbtor_other	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2275
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	2

Software

Software
Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling