2ZOM

Crystal structure of CutA1 from Oryza sativa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZFH	PDB ENTRY 2ZFH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	1.8M Ammonium sulfate, 0.09M tri-Sodium citrate dihydrate pH5.6, 0.18M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.214	α = 90
b = 127.214	β = 90
c = 121.868	γ = 90

Symmetry
Space Group	I 41 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	RIGAKU JUPITER 210	mirrors	2006-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1	SPring-8	BL26B1

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	3.02	63.628	100	0.061	0.061	8	10.3	10138	10138			76.463

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)
1	3.02	3.1	100		0.231	0.231	3.1	10.9	742

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZFH	3.02	63.61	9635	490	100	0.18237	0.18237	0.17826	0.19	0.26674	0.27	RANDOM	55.314

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]
0.78			0.78		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.699
r_dihedral_angle_3_deg	20.566
r_dihedral_angle_4_deg	17.239
r_dihedral_angle_1_deg	9.728
r_scangle_it	2.874
r_angle_refined_deg	2.204
r_scbond_it	1.956
r_mcangle_it	1.38
r_mcbond_it	1.097
r_angle_other_deg	1.023
r_symmetry_vdw_other	0.284
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.201
r_nbd_other	0.191
r_nbtor_refined	0.189
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.173
r_mcbond_other	0.162
r_chiral_restr	0.123
r_nbtor_other	0.099
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2534
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing