4ZKJ | pdb_00004zkj

Crystal structure of CRISPR-associated protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.6/0.6M Na/KH2PO4, 27% (w/v) glycerol and 130 mM HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
4.05	69.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.205	α = 90
b = 95.205	β = 90
c = 210.843	γ = 120

Symmetry
Space Group	P 31 2 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	ADSC QUANTUM 270		2014-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.9793	PAL/PLS	7A (6B, 6C1)

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	2.25	50	99.6	0.078	21.25	10.9	579853	579520

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	2.25	2.33	99.5		0.657	3.97	11.2

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	SAD	THROUGHOUT	2.25	35.14	546373	1961	97.6	0.18295	0.18185	0.19	0.21129	0.22	RANDOM	70.034

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]
0.37	0.18		0.37		-1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.251
r_dihedral_angle_4_deg	18.823
r_dihedral_angle_3_deg	13.311
r_long_range_B_other	9.841
r_long_range_B_refined	9.834
r_scangle_other	8.144
r_dihedral_angle_1_deg	5.91
r_scbond_it	5.66
r_scbond_other	5.66
r_mcangle_other	5.342
r_mcangle_it	5.341
r_mcbond_it	3.921
r_mcbond_other	3.9
r_angle_other_deg	2.429
r_angle_refined_deg	1.76
r_chiral_restr	0.109
r_bond_refined_d	0.019
r_gen_planes_other	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4657
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	phasing
PHENIX	model building
HKL-2000	data reduction