2HVF | pdb_00002hvf

Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	10 mM Imidazole (pH 8.0), 300 mM Zn Acetate, 3 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.517	α = 90
b = 53.517	β = 90
c = 36.178	γ = 90

Symmetry
Space Group	P 41 21 2

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 4		2006-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.1	NSLS	X26C

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	1.57	50	99.2	0.062	15.5	9.9	7705	7705

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	1.57	1.63	92.8		0.286		9.3	684

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Phase from wild type NTL9	THROUGHOUT	1.57	20	7670	7670	355	99.93	0.162	0.162	0.159	0.17	0.208	0.23	RANDOM	14.741

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]
0.02			0.02		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.887
r_dihedral_angle_3_deg	12.828
r_sphericity_free	8.58
r_scangle_it	4.461
r_dihedral_angle_1_deg	4.449
r_scbond_it	3.639
r_angle_other_deg	2.871
r_sphericity_bonded	2.454
r_mcangle_it	2.226
r_mcbond_it	1.974
r_rigid_bond_restr	1.732
r_angle_refined_deg	1.622
r_mcbond_other	0.568
r_symmetry_hbond_refined	0.392
r_xyhbond_nbd_refined	0.387
r_nbd_refined	0.269
r_metal_ion_refined	0.191
r_nbtor_refined	0.185
r_nbd_other	0.173
r_symmetry_vdw_other	0.142
r_symmetry_vdw_refined	0.108
r_nbtor_other	0.102
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	400
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	17

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	phasing