2BKF | pdb_00002bkf

Structure of the PB1 domain of NBR1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.1		1.6 M AMMONIUM SULFATE,0.1 M SODIUM ACETATE PH 4.1

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.612	α = 90
b = 100.612	β = 90
c = 42.16	γ = 120

Symmetry
Space Group	P 63 2 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	MARRESEARCH	MIRROR	2003-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	1.56	20	99.6	0.06	46.6	18.9		18381		-3

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	1.55	1.61	100		0.59	4.8

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	MAD	THROUGHOUT	1.56	21.78	17183	923	97.7	0.2	0.199	0.21	0.226	0.23	RANDOM	36.66

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]
-0.66	-0.33		-0.66		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.819
r_dihedral_angle_3_deg	13.314
r_dihedral_angle_1_deg	5.665
r_scangle_it	3.514
r_scbond_it	2.61
r_mcangle_it	2.453
r_mcbond_it	2.118
r_angle_refined_deg	1.484
r_angle_other_deg	0.734
r_symmetry_hbond_refined	0.233
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.21
r_nbtor_refined	0.173
r_symmetry_vdw_other	0.173
r_nbd_other	0.168
r_xyhbond_nbd_refined	0.168
r_nbtor_other	0.09
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	687
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing